BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0256.0059.p (445 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_242502.1| 30S ribosomal protein S1 [Bacillus halodurans] ... 363 6e-99 ref|NP_977946.1| ribosomal protein S1 [Bacillus cereus ATCC 1098... 346 8e-94 ref|NP_655400.1| S1, S1 RNA binding domain [Bacillus anthracis A... 345 1e-93 ref|NP_831277.1| SSU ribosomal protein S1P [Bacillus cereus ATCC... 343 4e-93 ref|NP_390169.1| alternate gene name: jofD~similar to ribosomal ... 338 2e-91 >ref|NP_242502.1| 30S ribosomal protein S1 [Bacillus halodurans] pir||D83854 hypothetical protein BH1636 [imported] - Bacillus halodurans (strain C-125) dbj|BAB05355.1| 30S ribosomal protein S1 [Bacillus halodurans] Length = 383 Score = 363 bits (931), Expect = 6e-99, Method: Compositional matrix adjust. Identities = 194/389 (49%), Positives = 251/389 (64%), Gaps = 16/389 (4%) Query: 54 EIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXXXXXXXXXXXC 113 E+ S GD V G + K+ED QA+V +G+K DG+IPI ELSS+ ++ Sbjct: 11 EMKSFSVGDVVSGKVTKVEDKQAFVDVGFKVDGIIPISELSSLHVEKVSDVLSEGDELEL 70 Query: 114 KVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGLVADVGARGFI 173 KV+ + D++ L+LSKRAV +EK+WE L+ S E E VADVVKGGLV D+G RGFI Sbjct: 71 KVLKVEDDE--LILSKRAVQAEKAWETLQAALDSGEVIEAEVADVVKGGLVVDLGVRGFI 128 Query: 174 PASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEANKQKIMSELSE 233 PAS+VERH+VEDFSDYKGRTLR+KV ELD+E +K+ILS + VL+EE EA K+++++ L Sbjct: 129 PASLVERHYVEDFSDYKGRTLRLKVVELDKEANKLILSQRAVLDEEVEAKKKEVLASLQP 188 Query: 234 GQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXXXXXXXXXXXXX 293 G ++EGTVQRLT FGAF LVH+S++A + VE P++ Sbjct: 189 GDVVEGTVQRLTDFGAFVDVGGVDGLVHISQLAHHRVETPAEVVKEGDAVKVKVLSVDPD 248 Query: 294 XGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGVEGLVHISQISH 353 ++SLSIK PGPW+ G I GDV+ G VKRLV+FGAFVE+ PGVEGLVHISQI++ Sbjct: 249 SERVSLSIKETLPGPWEQVEGTIQPGDVIEGTVKRLVSFGAFVEVAPGVEGLVHISQIAN 308 Query: 354 KHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIKXXXXXXXXXXXXXXSNNRDRAPKEV 413 +HIGTP EVL EG+ VQ KVLD N SEKR+SLSI+ SN DR EV Sbjct: 309 RHIGTPGEVLSEGERVQAKVLDVNISEKRISLSIR-------ELLDDAGSNQSDR---EV 358 Query: 414 LNNPNVSLSNEGLSFTLAERFGDKLDKFK 442 + N E F+L + GD+L K+K Sbjct: 359 YESTN----EESSGFSLGDMIGDELKKYK 383 >ref|NP_977946.1| ribosomal protein S1 [Bacillus cereus ATCC 10987] sp|O06000|RS1H_BACCE 30S RIBOSOMAL PROTEIN S1 HOMOLOG emb|CAA70584.1| 30S ribosomal protein S1 [Bacillus cereus] gb|AAS40554.1| ribosomal protein S1 [Bacillus cereus ATCC 10987] Length = 382 Score = 346 bits (887), Expect = 8e-94, Method: Compositional matrix adjust. Identities = 177/346 (51%), Positives = 241/346 (69%), Gaps = 8/346 (2%) Query: 43 NEEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXX 102 NEE + S+E L+ GD V G++ K+E+ Q V++GYK DGVIPI EL++V ++ Sbjct: 6 NEEVMDSKE------LQVGDVVTGSVTKVEEKQVLVNVGYKTDGVIPISELANVHIEKAS 59 Query: 103 XXXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGG 162 K++ + +N LVLSKRAVD+EK+W +L++ F S F+VTV D+V GG Sbjct: 60 DVVELDQILELKIIKLEEN--DLVLSKRAVDAEKAWIELQEKFTSGHVFDVTVKDIVNGG 117 Query: 163 LVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEA 222 LV D+G RGFIPAS+VE H+VEDF+DYKG+TL VK+ ELDRE ++VILS K V+E E ++ Sbjct: 118 LVVDLGVRGFIPASLVEVHYVEDFTDYKGKTLAVKIVELDREKNRVILSHKAVVELELDS 177 Query: 223 NKQKIMSELSEGQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXX 282 K++ +S L EG ++EGTVQRLT FGAF LVH+S+I+ VE+PS+ Sbjct: 178 KKKEAISSLKEGDVVEGTVQRLTDFGAFVNVGGVDGLVHISQISHERVEQPSEVLEQGQK 237 Query: 283 XXXXXXXXXXXXGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGV 342 +ISLSIKAA PGPW++ AG++ GD+ G VKRLV FGAFVE+LPGV Sbjct: 238 VKVKVLSVDADTQRISLSIKAAQPGPWENIAGEVKAGDIREGIVKRLVTFGAFVEILPGV 297 Query: 343 EGLVHISQISHKHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIK 388 EGLVH+SQI+++H+ P+EVL+ GQEV+VKVL+ + +EKR+SLSIK Sbjct: 298 EGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHVAEKRISLSIK 343 >ref|NP_655400.1| S1, S1 RNA binding domain [Bacillus anthracis A2012] ref|NP_843970.1| ribosomal protein S1 [Bacillus anthracis str. Ames] gb|AAP25456.1| ribosomal protein S1 [Bacillus anthracis str. Ames] Length = 382 Score = 345 bits (884), Expect = 1e-93, Method: Compositional matrix adjust. Identities = 177/346 (51%), Positives = 240/346 (69%), Gaps = 8/346 (2%) Query: 43 NEEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXX 102 NEE + S+E L+ GD V G++ K+E+ Q V++GYK DGVIPI EL++V ++ Sbjct: 6 NEEVMDSKE------LQVGDVVTGSVTKVEEKQVLVNVGYKTDGVIPISELANVHIEKAS 59 Query: 103 XXXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGG 162 KV+ + +N LVLSKRAVD+EK+W +L++ F S F+VTV D+V GG Sbjct: 60 DVVELDQTLELKVIKLEEN--DLVLSKRAVDAEKAWVELQEKFNSGHVFDVTVKDIVNGG 117 Query: 163 LVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEA 222 LV D+G RGFIPAS+VE H+VEDF+DYKG+TL VK+ ELDRE ++VILS K V+E E ++ Sbjct: 118 LVVDLGVRGFIPASLVEVHYVEDFTDYKGKTLAVKIVELDREKNRVILSHKAVVELELDS 177 Query: 223 NKQKIMSELSEGQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXX 282 K++ +S L EG ++EGTVQRLT FGAF LVH+S+I+ VE+PS+ Sbjct: 178 KKKEAISSLKEGDVVEGTVQRLTDFGAFVNVGGVDGLVHISQISHERVEQPSEVLEQGQK 237 Query: 283 XXXXXXXXXXXXGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGV 342 +ISLSIKAA PGPW++ G++ GD+ G VKRLV FGAFVE+LPGV Sbjct: 238 VKVKVLSVDADTQRISLSIKAAQPGPWENVGGEVKAGDIREGVVKRLVTFGAFVEILPGV 297 Query: 343 EGLVHISQISHKHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIK 388 EGLVH+SQI+++H+ P+EVL+ GQEV+VKVL+ + +EKR+SLSIK Sbjct: 298 EGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHVAEKRISLSIK 343 Score = 53.9 bits (128), Expect = 8e-06, Method: Compositional matrix adjust. Identities = 52/202 (25%), Positives = 100/202 (49%), Gaps = 14/202 (6%) Query: 44 EEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXX 103 E E+ S++ I SLK+GD V+GT+ ++ D A+V++G DG++ I ++S +++ Sbjct: 172 ELELDSKKKEAISSLKEGDVVEGTVQRLTDFGAFVNVG-GVDGLVHISQISHERVEQPSE 230 Query: 104 XXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGL 163 KV+S++ + + + LS +A WE++ + + E V +V G Sbjct: 231 VLEQGQKVKVKVLSVDADTQRISLSIKAAQP-GPWENVGGEVKAGDIREGVVKRLVTFGA 289 Query: 164 VADV--GARGFIPASMVERHFVEDFSDY--KGRTLRVKVKELDRENSKVILSAKEVLEE- 218 ++ G G + S + V++ ++ G+ ++VKV E+ ++ LS KE LEE Sbjct: 290 FVEILPGVEGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHVAEKRISLSIKEALEEN 349 Query: 219 -------EFEANKQKIMSELSE 233 ++E N +LS+ Sbjct: 350 NVTEDYSQYEPNADSATFQLSD 371 >ref|NP_831277.1| SSU ribosomal protein S1P [Bacillus cereus ATCC 14579] gb|AAP08478.1| SSU ribosomal protein S1P [Bacillus cereus ATCC 14579] Length = 382 Score = 343 bits (881), Expect = 4e-93, Method: Compositional matrix adjust. Identities = 176/346 (50%), Positives = 240/346 (69%), Gaps = 8/346 (2%) Query: 43 NEEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXX 102 NEE + S+E L+ GD V G++ K+E+ Q V++GYK DGVIPI EL++V ++ Sbjct: 6 NEEVMDSKE------LQVGDVVTGSVTKVEEKQVLVNVGYKTDGVIPISELANVHIEKAS 59 Query: 103 XXXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGG 162 K++ + ++ LVLSKRAVD+EK+W +L++ F S F+V V D+V GG Sbjct: 60 DVVELDQTLELKIIKLEED--DLVLSKRAVDAEKAWVELQEKFTSGHVFDVIVKDIVNGG 117 Query: 163 LVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEA 222 LV D+G RGFIPAS+VE H+VEDF+DYKG+TL VK+ ELDRE ++VILS K V+E E ++ Sbjct: 118 LVVDLGVRGFIPASLVEVHYVEDFTDYKGKTLAVKIVELDREKNRVILSHKAVVELELDS 177 Query: 223 NKQKIMSELSEGQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXX 282 K++ +S L EG ++EGTVQRLT FGAF LVH+S+I+ VE+PS+ Sbjct: 178 KKKEAISSLKEGDVVEGTVQRLTDFGAFVNVGGVDGLVHISQISHERVEQPSEVLEQGQK 237 Query: 283 XXXXXXXXXXXXGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGV 342 +ISLSIKAA PGPW++ AG+I GD+ G VKRLV FGAFVE+LPGV Sbjct: 238 VKVKVLSVDADTQRISLSIKAAQPGPWENVAGEIKAGDIREGVVKRLVTFGAFVEILPGV 297 Query: 343 EGLVHISQISHKHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIK 388 EGLVH+SQI+++H+ P+EVL+ GQEV+VKVL+ + +EKR+SLSIK Sbjct: 298 EGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHVAEKRISLSIK 343 Score = 54.3 bits (129), Expect = 5e-06, Method: Compositional matrix adjust. Identities = 52/202 (25%), Positives = 100/202 (49%), Gaps = 14/202 (6%) Query: 44 EEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXX 103 E E+ S++ I SLK+GD V+GT+ ++ D A+V++G DG++ I ++S +++ Sbjct: 172 ELELDSKKKEAISSLKEGDVVEGTVQRLTDFGAFVNVG-GVDGLVHISQISHERVEQPSE 230 Query: 104 XXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGL 163 KV+S++ + + + LS +A WE++ + + E V +V G Sbjct: 231 VLEQGQKVKVKVLSVDADTQRISLSIKAAQP-GPWENVAGEIKAGDIREGVVKRLVTFGA 289 Query: 164 VADV--GARGFIPASMVERHFVEDFSDY--KGRTLRVKVKELDRENSKVILSAKEVLEE- 218 ++ G G + S + V++ ++ G+ ++VKV E+ ++ LS KE LEE Sbjct: 290 FVEILPGVEGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHVAEKRISLSIKEALEEN 349 Query: 219 -------EFEANKQKIMSELSE 233 ++E N +LS+ Sbjct: 350 NVTEDYSQYEPNADSATFQLSD 371 >ref|NP_390169.1| alternate gene name: jofD~similar to ribosomal protein S1 homolog [Bacillus subtilis] sp|P38494|RS1H_BACSU 30S ribosomal protein S1 homolog pir||B69935 ribosomal protein S1 homolog ypfD - Bacillus subtilis gb|AAA85150.1| unknown gb|AAC83962.1| similar to Escherichia coli S1 ribosomal protein; putative [Bacillus subtilis] emb|CAB14204.1| ypfD [Bacillus subtilis subsp. subtilis str. 168] Length = 382 Score = 338 bits (866), Expect = 2e-91, Method: Compositional matrix adjust. Identities = 184/383 (48%), Positives = 239/383 (62%), Gaps = 17/383 (4%) Query: 61 GDTVKGTIVKIEDNQAYVSI-GYKYDGVIPIRELSSVQLDNXXXXXXXXXXXXCKVVSIN 119 GD VKG + K+ED V I K G+IPI ELSS+ ++ KV + Sbjct: 16 GDVVKGIVTKVEDKHVDVEIINVKQSGIIPISELSSLHVEKASDVVKVDDELDLKVTKVE 75 Query: 120 DNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGLVADVGARGFIPASMVE 179 D+ +L+LSKRAVD++++WEDLEK F ++E FE V DVVKGGLV D+G RGFIPAS+VE Sbjct: 76 DD--ALILSKRAVDADRAWEDLEKKFETKEVFEAEVKDVVKGGLVVDIGVRGFIPASLVE 133 Query: 180 RHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEANKQKIMSELSEGQIIEG 239 HFVEDF+DYKG+TL + V ELDR+ ++VILS + V+E E KQ+++ L G +++G Sbjct: 134 AHFVEDFTDYKGKTLSLLVVELDRDKNRVILSHRAVVESEQANKKQELLQSLEVGSVLDG 193 Query: 240 TVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXXXXXXXXXXXXXXGKISL 299 VQRLT FGAF LVH+S+++ +HVEKPSD +ISL Sbjct: 194 KVQRLTDFGAFVDIGGIDGLVHISQLSHSHVEKPSDVVEEGQEVKVKVLSVDRDNERISL 253 Query: 300 SIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGVEGLVHISQISHKHIGTP 359 SIK PGPW+ K+ GDV+ G V+RLV+FGAFVE+LPGVEGLVHISQIS+KHIGTP Sbjct: 254 SIKDTLPGPWNQIGEKVKPGDVLEGTVQRLVSFGAFVEILPGVEGLVHISQISNKHIGTP 313 Query: 360 HEVLKEGQEVQVKVLDFNPSEKRVSLSIKXXXXXXXXXXXXXXSNNRDRAPKEVLNNPNV 419 HEVL+EGQ V+VKVLD N +E+R+SLS++ + R KE Sbjct: 314 HEVLEEGQTVKVKVLDVNENEERISLSMR----ELEETPKADQEDYRQYQAKE------- 362 Query: 420 SLSNEGLSFTLAERFGDKLDKFK 442 F L + GDKL+K K Sbjct: 363 ---ETSTGFQLGDLIGDKLNKLK 382 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.312 0.131 0.358 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 495,766,264 Number of extensions: 17466113 Number of successful extensions: 49236 Number of sequences better than 1.0e-05: 1480 Number of HSP's gapped: 45508 Number of HSP's successfully gapped: 2055 Length of query: 445 Length of database: 757,237,578 Length adjustment: 129 Effective length of query: 316 Effective length of database: 406,989,807 Effective search space: 128608779012 Effective search space used: 128608779012 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 127 (53.5 bits)