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= 0092.0048.p (506 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein [Herbas... 357 1e-99 gi|300311262|ref|YP_003775354.1| DNA repair protein [Herbaspiril... 284 1e-77 gi|300311260|ref|YP_003775352.1| dsRNA-specific ribonuclease [He... 196 3e-51 gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/fu... 69 6e-13 gi|300312253|ref|YP_003776345.1| GTP-binding protein [Herbaspiri... 67 3e-12 >gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 357 bits (916), Expect = 1e-99, Method: Compositional matrix adjust. Identities = 180/256 (70%), Positives = 205/256 (80%), Gaps = 16/256 (6%) Query: 142 MTELNAPSDAS-----SDYRCGYIAIVGRPNVGKSTLMNVLIGAKVSITSRKAQTTRHRI 196 MT+ DAS SDYRCGYIAIVGRPNVGKSTLMNVL+GAKVSITSRKAQTTRHRI Sbjct: 1 MTDSPMADDASAQTPDSDYRCGYIAIVGRPNVGKSTLMNVLVGAKVSITSRKAQTTRHRI 60 Query: 197 TGIQTIDNTQFVYVDTPGFQTRHSNALNKTLNRTVTSTLTAADVILYVIEAGTFGPADKQ 256 TGIQTI+NTQ+VYVDTPGFQTRHSNALNKTLNRTVT+TLTAADVIL+VIEAGTFGPADKQ Sbjct: 61 TGIQTIENTQYVYVDTPGFQTRHSNALNKTLNRTVTNTLTAADVILFVIEAGTFGPADKQ 120 Query: 257 VMELLPANVPCILVMNKSDRSKDKSVLMPFAQEVASQHNFASVVPVSAKQRFQLDALQDE 316 V++LLPANVPCILV+NK+DR+KDK+ LMPFA+EVAS H+FA+VVPVSAKQRFQLD LQ+E Sbjct: 121 VLDLLPANVPCILVLNKADRNKDKTTLMPFAREVASHHDFAAVVPVSAKQRFQLDRLQEE 180 Query: 317 IRKLLPVNPPMFDEDDITDGXVRTLTAA-------EWVGGLLPLEKSALLCGFY----LN 365 +RKLLP NPPMFDEDDITD + L + +VG LP + L+ F L Sbjct: 181 VRKLLPQNPPMFDEDDITDRSEKFLASEIVREKVFRFVGEELPYTSTVLIEKFEQEGNLR 240 Query: 366 ELLVKLLAREDAHPAL 381 + +L D H A+ Sbjct: 241 RIFAAILVERDNHKAM 256 >gi|300311262|ref|YP_003775354.1| DNA repair protein [Herbaspirillum seropedicae SmR1] Length = 286 Score = 284 bits (727), Expect = 1e-77, Method: Compositional matrix adjust. Identities = 138/169 (81%), Positives = 148/169 (87%) Query: 338 VRTLTAAEWVGGLLPLEKSALLCGFYLNELLVKLLAREDAHPALFDHYVSTLNQLAHGES 397 VRTLT AEWVGGLLPLEKSALLCGFYLNELLVKLLAREDAHPALFDHYV+TLN+LAHGE+ Sbjct: 118 VRTLTDAEWVGGLLPLEKSALLCGFYLNELLVKLLAREDAHPALFDHYVATLNKLAHGEN 177 Query: 398 TPIVLRKFERALLKETGVAGDWTVCVTNGKPVAPDDTYVVDPEQGVRFPRLSDAWPKVSG 457 PIVLR+FER LLK+TGVAG+W+ CV +GK V PD YVVDPEQG R RLSD PKVSG Sbjct: 178 APIVLRQFERILLKQTGVAGNWSHCVVSGKTVRPDLIYVVDPEQGTRPERLSDRAPKVSG 237 Query: 458 KTLLDMEKEDYSDAATQSQSKLLMRSLLSHHLGGTQLNTRQILIDLSQL 506 KTLLDME+EDYSD TQ QSK LMR LL+HHLGG QLNTRQILIDL QL Sbjct: 238 KTLLDMEREDYSDPTTQLQSKFLMRYLLAHHLGGAQLNTRQILIDLMQL 286 >gi|300311260|ref|YP_003775352.1| dsRNA-specific ribonuclease [Herbaspirillum seropedicae SmR1] Length = 319 Score = 196 bits (499), Expect = 3e-51, Method: Compositional matrix adjust. Identities = 92/102 (90%), Positives = 99/102 (97%) Query: 1 MDPLVLQNRLGHNFKDATLLQQALTHRSHSSLHNERLEFLGDSILNCVVASLLFDRYNKI 60 MDP +LQ RLGH FKDA+LLQQALTHRSHS+LHNERLEFLGDS+LNCVVASLLF+RY+KI Sbjct: 1 MDPQLLQQRLGHTFKDASLLQQALTHRSHSALHNERLEFLGDSVLNCVVASLLFERYDKI 60 Query: 61 DEGDLSRLRANLVKQQSLYEIAQRLDLSQFLRLGEGELKSGG 102 DEGDLSRLRANLVKQQSLYEIAQRL+LSQFLRLGEGELKSGG Sbjct: 61 DEGDLSRLRANLVKQQSLYEIAQRLELSQFLRLGEGELKSGG 102 >gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/furan oxidation) GTPase [Herbaspirillum seropedicae SmR1] Length = 479 Score = 69.3 bits (168), Expect = 6e-13, Method: Compositional matrix adjust. Identities = 48/139 (34%), Positives = 74/139 (53%), Gaps = 12/139 (8%) Query: 162 IVGRPNVGKSTLMNVLIGAKVSITSRKAQTTRHRITGIQTIDNTQFVYVDTPGFQTRHSN 221 + G+PNVGKS+L+NVL G+ V+I + A TTR ++T I+ +DT G + + Sbjct: 239 LAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTQTIQIEGMPLNIIDTAGIREAGDD 298 Query: 222 ALNK------TLNRTVTSTLTAADVILYVIEAGTFGPA--DKQVMELLPANVPCILVMNK 273 + RT + + ADVIL++++A GP D+++ P VP I + NK Sbjct: 299 GSGPDEVERIGIERT-WAEVAKADVILHMLDADR-GPTLEDEKITSRFPDGVPIIRIWNK 356 Query: 274 SDRSKDKSVL--MPFAQEV 290 DRS K+ + MP A V Sbjct: 357 IDRSGHKAAVDKMPDATHV 375 >gi|300312253|ref|YP_003776345.1| GTP-binding protein [Herbaspirillum seropedicae SmR1] Length = 447 Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 41/131 (31%), Positives = 68/131 (51%), Gaps = 2/131 (1%) Query: 160 IAIVGRPNVGKSTLMNVLIGAKVSITSRKAQTTRHRITGIQTIDNTQFVYVDTPGFQTRH 219 IA+VGRPNVGKSTL N L ++ ++ + TR R G + F+ +DT GF+ Sbjct: 5 IALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGFEPVA 64 Query: 220 SNALNKTLNRTVTSTLTAADVILYVIEA-GTFGPADKQVMELL-PANVPCILVMNKSDRS 277 + + + + + ADV++++++ P DK + + L P +LV+NKS+ Sbjct: 65 KDGIMYEMAKQTKQAVVEADVVVFIVDGRQGLTPHDKTITDFLRKCGRPVLLVVNKSEGM 124 Query: 278 KDKSVLMPFAQ 288 K SV F + Sbjct: 125 KYTSVTADFYE 135 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.318 0.134 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,428,292 Number of extensions: 54847 Number of successful extensions: 221 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 220 Number of HSP's successfully gapped: 5 Length of query: 506 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 417 Effective length of database: 1,198,455 Effective search space: 499755735 Effective search space used: 499755735 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 133 (55.8 bits)