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= 0229.0042.p (533 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter perip... 400 e-112 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 152 8e-38 gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter perip... 148 9e-37 gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter perip... 94 4e-20 gi|300312719|ref|YP_003776811.1| oligopeptide ABC transporter pe... 84 2e-17 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 400 bits (1028), Expect = e-112, Method: Compositional matrix adjust. Identities = 210/479 (43%), Positives = 295/479 (61%), Gaps = 4/479 (0%) Query: 44 FAD-VSTLDPHFNNIAPNISLSSHLFDALVNVDATGKLIPGLAVSWKAIDPTTWEFKLRR 102 FAD +S+LDP NN A + S+ H +D LV D KL+PGLAVSWK IDP TWEFKLR Sbjct: 35 FADPLSSLDPQLNNHAGDRSVDLHFWDLLVQND-YNKLVPGLAVSWKNIDPKTWEFKLRP 93 Query: 103 GVKFHDGSDFTAEDVVFSLDRPATLTNSPGPFTSYTKQIVGKEIVDPYTVRLKTATPYGP 162 VK+ DG FTA+DV+FS R + S F Y + + DP T+ +KT P Sbjct: 94 NVKWQDGKPFTADDVIFSYQRARAVPGSVATFAGYLRTVESVTAKDPLTLVIKTNIPNPD 153 Query: 163 LALDVSTIFIVSKKAAQNATTEDFNSGKALIGTGPFKFGNFERGDSIELVRNDSYWGGKA 222 L L+++++ IVSK + +TTE++NSG A+IGTGP+KF ++ GD + + RND YW GK Sbjct: 154 LPLNLASVHIVSKHIGEKSTTENYNSGAAVIGTGPYKFVSYTPGDRVVMQRNDDYWNGKP 213 Query: 223 DWDKVTFRILTSDGARLAALLAGEVDAIDSVPPADVPKLKTNPKFSLVQRTSWRTIFWTL 282 W+KV +R + + AR AALL+G+VD ID V +D+ KLK +P + R + Sbjct: 214 LWEKVNYRYINNGAARTAALLSGDVDVIDKVSVSDLAKLKQSPNVKVYPYNGLRVLLIQP 273 Query: 283 DQSRDKTPDITDKSGKPLDKNPLKDIRVRQAISKAINRQALTERTLEGLGTPASNIVAPG 342 + +P ITD +GK LDKNPL D+RVR+A+S AINR+AL +R L+G T A+ + Sbjct: 274 SFHQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKALIDRILQGAATEANQWMPAD 333 Query: 343 ILGYADKLKVEKYDPEGAKKLLAEAGYPNGFALTLHGPNNRYINDERVVQTVAQFLSRVG 402 GY ++K +D AKKLLA+AG+P+GF LT+H PN+RY +Q VAQF +R+G Sbjct: 334 TFGYNPEIKNIPFDAAQAKKLLADAGFPDGFKLTIHVPNDRYPQAPETMQAVAQFWTRIG 393 Query: 403 IQTKVETFPLSVYFGKARNGDFSVALLGWGTLAGD--FGLRTLVGTTDAATGWGSWNWGK 460 I+T+VE P + Y +A +F+V++L WG G+ + L ++G+ D G G+ NW Sbjct: 394 IKTQVEVLPWAAYSSRANKNEFAVSVLAWGNGTGEASYALVNVLGSVDPKKGIGASNWNH 453 Query: 461 YSNPQVDKLVQSSLSSVDEKQRQDFAQQAATVALNDYAVIPLHHQYATWAVRKGLKYTP 519 YS+P VDK + S + D +R+ + AA + VIPL+H WA +KGLK TP Sbjct: 454 YSSPAVDKALADSTAEFDAAKREAILRGAAKTVSEEVGVIPLYHYQNIWAAKKGLKVTP 512 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 152 bits (383), Expect = 8e-38, Method: Compositional matrix adjust. Identities = 132/492 (26%), Positives = 217/492 (44%), Gaps = 42/492 (8%) Query: 45 ADVSTLDPHFNNIAPNISLSSHLFDALVNVD-ATGKLIPGLAVSWKAIDPTTWEFKLRRG 103 ++V + + NN+ + L+ ++D L+ D T + P LA +WK PT LR+G Sbjct: 42 SEVENISQYHNNLREGVILAHLIWDTLIYRDPKTNEYKPQLATAWKWESPTALVLDLRQG 101 Query: 104 VKFHDGSDFTAEDVVFSLDRPATLTNSPGPFTSYTKQIVGKEIVDPYTVRLKTATPYGPL 163 V+F +G F+A+DVVF+ + A S T I + + Y VR+ P+ P Sbjct: 102 VQFQNGDKFSADDVVFTFNY-AVSPESKAVTRQNTDWIKSVDKLADYKVRINLKGPF-PA 159 Query: 164 ALD--VSTIFIVSKKAAQNATTEDFNSGKALIGTGPFKFGNFERGDSIELVRNDSYWG-- 219 AL+ + I + E F+ KA IGTGP+K + G + LV+N Y+ Sbjct: 160 ALEYLAGPLPIYPAAYFKKVGLEGFS--KAPIGTGPYKVTSVTPGQGVTLVKNPGYFKDS 217 Query: 220 --GKADWDKVTFRILTSDGARLAALLAGEVDAIDSVPPADVPKLKTNPKFSLVQRTSWRT 277 G+ + F ++ R A L+ G +D I VPP LKTNPK ++ + R Sbjct: 218 PQGQPTIGNIKFVVIPDPETRAAQLMTGAIDWIWRVPPDQADSLKTNPKLAVQSGETMRI 277 Query: 278 IFWTLDQSRDKTPDITDKSGKPLDKNPLKDIRVRQAISKAINRQALTERTLEGLGTPASN 337 F TLD + P+ +P KD+RVRQA++ AINR+ + + G P Sbjct: 278 GFITLDTTGTSAPN-----------SPFKDVRVRQAVNHAINRKGYADNLMRGGSQPVYT 326 Query: 338 IVAPGILGYADKLKVE-KYDPEGAKKLLAEAGYPNGFALTLHGPNNRYINDERVVQTVAQ 396 G ++ Y+P AK+LLA AGYPNGF ++ R + + + Sbjct: 327 ACFRTQFGCDSNAAIKYDYNPAKAKELLAAAGYPNGFDTDIYAYRER-----EIAEAIIG 381 Query: 397 FLSRVGIQTKVETFPLSVYFGKARNGDFSVALLGWGTLAGD----FGLRTLVGTTDAATG 452 L +VGI+ ++ + + R+G ++ WG+ + + F G D T Sbjct: 382 DLRKVGIRARLHYMKFAALQTEYRSGKTPMSFYSWGSFSMNDTSAFAGVYFKGGADDIT- 440 Query: 453 WGSWNWGKYSNPQVDKLVQSSLSSVDEKQRQDFAQQAATVALNDYAVIPLHHQYATWAVR 512 +PQ+ + +Q++ +S+D R+ +A + V P+ +A Sbjct: 441 ---------KDPQLQQYLQTADTSIDPAVRKANYSKAQELISKQAYVAPMFSYSTYYAYN 491 Query: 513 KGLKYTPRIDEF 524 L + DE Sbjct: 492 AQLNFQGYPDEL 503 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 148 bits (374), Expect = 9e-37, Method: Compositional matrix adjust. Identities = 126/463 (27%), Positives = 213/463 (46%), Gaps = 39/463 (8%) Query: 41 LGLFADVSTLDPHFNNIAPNISLSSHLFDALVNVDATGKLIPGLAVSW-KAIDPTTWEFK 99 L +++ +TLDP+ N ++S++ + L D KLIP LA + + D + + Sbjct: 40 LAVYSTFTTLDPYDANDTLSLSMAKSFYQGLFGFDKDMKLIPVLAEGYLVSKDGLEYTIR 99 Query: 100 LRRGVKFHDGSDFTAEDVVFSLDRPATLTNSPGPFTSYT--KQIVGKEIVDPYTVRLKTA 157 L++GVKF DG+ F A+ V DR +TN Y +I EI++ YTV++ Sbjct: 100 LKQGVKFQDGTVFKADAVKAVFDR---VTNPDNKLKRYNLFNRIAKTEILNDYTVKVVLK 156 Query: 158 TPYGPL--ALDVSTIFIVSKKAAQNATTEDFNSGKALIGTGPFKFGNFERGDSIELVRND 215 P+ L + ++S A + +D +GTGPFKF +++ D +++ + D Sbjct: 157 EPFSAFINVLAHPSAVMISPTALKQYGNKDIAFHP--VGTGPFKFVEWKQTDYVKVAKFD 214 Query: 216 SYWG-GKADWDKVTFRILTSDGARLAALLAGEVDAIDSVPPADVPKLKTNPKFSLVQRTS 274 YW G D++ ++ + + AR A + GE +P LK+ +V S Sbjct: 215 GYWKPGYPKVDEIIWKPVVDNNARSAMMQTGEAQFTYPLPYEQADLLKSKSNLDVVAAPS 274 Query: 275 WRTIFWTLDQSRDKTPDITDKSGKPLDKNPLKDIRVRQAISKAINRQALTERTLEGLGTP 334 + +++ + KP D NP +VR+AI+ AIN+QAL + G P Sbjct: 275 IIQRYMSMNTKQ-----------KPFD-NP----KVREAINYAINKQALVKVAFNGYAVP 318 Query: 335 ASNIVAPGILGYADKLKVEKYDPEGAKKLLAEAGYPNGFALTLHGPNNRYINDERVVQTV 394 +V G+ YA K YD + AK LLAEAGYPNGF L + ++VQ + Sbjct: 319 MDGVVPQGV-DYAYKTGPWPYDVKKAKALLAEAGYPNGFETELWSAYT-HSTAVKIVQFL 376 Query: 395 AQFLSRVGIQTKVETFPLSVYFGKARN------GDFSVALLGWGTLAG--DFGLRTLVGT 446 Q L++VGI+ K++ + + + +GW + G D+ LR L+ + Sbjct: 377 QQQLAQVGIKAKIQALEAGQRVERVESWQDPATAPVRLLYIGWSSSTGEADWALRPLLAS 436 Query: 447 TDAATGWGSWNWGKYSNPQVDKLVQSSLSSVDEKQRQDFAQQA 489 +N Y N +VD + +L+ + K ++ + A Sbjct: 437 ESFPPRL--YNTAYYKNDKVDADIAKALTLTERKDKEALYKDA 477 >gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter periplasmic peptide-binding protein [Herbaspirillum seropedicae SmR1] Length = 540 Score = 93.6 bits (231), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 115/485 (23%), Positives = 203/485 (41%), Gaps = 56/485 (11%) Query: 13 LLSLAFTGL--AAAAVLPLTAQSSLAAELKLGLFADVSTLDPHFNNIAPNISLSSHLFDA 70 L+++ TGL A+ +V+ T + + + TLDP + + + ++ Sbjct: 42 LMTVGGTGLLTASGSVMAQTGKRGGKMRIATQTSSTADTLDPAKTAHSTDYTRVHMFYNG 101 Query: 71 LVNVDATGKLIPGLAVSWKAI--DPTTWEFKLRRGVKFHDGSDFTAEDVVFSLDR---PA 125 L +D GKL P + ++ + + D TW KLR+GV FHDG T DVV+S+ R PA Sbjct: 102 LTKLD--GKLGPQMVLAEEMLTNDAVTWTVKLRKGVNFHDGKPLTPADVVYSIMRHKDPA 159 Query: 126 TLTNSPGPFTSYTKQIVGKEIVDPYTVRLKTATPYGPLALDVSTI-FIVSKKAAQNATTE 184 T + Q + P V++K + L + ++T F++ + N +T Sbjct: 160 TASK----VKVVADQFESVKATGPNEVQIKLTSANADLPVILATAQFLIIRDGTTNFSTP 215 Query: 185 DFNSGKALIGTGPFKFGNFERGDSIELVRNDSYWG-GKADWDKVTFRILTSDGARLAALL 243 + GTG FK F G VRN++YW G D+V + + AR+ ALL Sbjct: 216 N--------GTGAFKLKEFTPGVRTIGVRNENYWKPGLPYLDEVELFGIPDEAARVNALL 267 Query: 244 AGEVDAIDSVPPADVPKLKTNPKFSLVQRTSWRTIFWTLDQSRDKTPDITDKSGKPLDKN 303 +G+V I+ V ++K P +++++ S + + Q D Sbjct: 268 SGDVHWINDVNSRSTGRVKNTPGYTVMETKSGQYTDLVMRQ----------------DVA 311 Query: 304 PLKDIRVRQAISKAINRQALTERTLEGLGTPASNI-VAPGILGYADKLKVEKYDPEGAKK 362 P + + ++R+ + G A++ + P Y L YDP+ AK Sbjct: 312 PGNSMDFTLGMKYLLDREQIKMAAFRGYAVIANDQPIDPTNRFYFAGLPQRPYDPDKAKF 371 Query: 363 LLAEAGYPNGFALTLHGPNNRYINDERVVQTVAQFLSRVGIQTKVETFPLSVYFGKARNG 422 L +AG + D V+ + Q +++G++ V+ P Y+ + Sbjct: 372 HLGKAGVLGSTIPIVASVAATGSVDMAVL--MQQSAAKIGLKLDVKRVPADGYW----SN 425 Query: 423 DFSVALLGWGTL----AGDFGLRTLVGTTDAATGWGSWNWGKYSNPQVDKLVQSSLSSVD 478 + +G+G + + D L T +DA WN + NPQ D+LV ++ D Sbjct: 426 QWMKVPVGFGNINPRPSADI-LLTQFFKSDA-----QWNESGWKNPQFDQLVVAARGETD 479 Query: 479 EKQRQ 483 +R+ Sbjct: 480 FTKRK 484 >gi|300312719|ref|YP_003776811.1| oligopeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 609 Score = 84.3 bits (207), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 124/474 (26%), Positives = 196/474 (41%), Gaps = 73/474 (15%) Query: 90 AIDPTTWEFKLRRGVKFHDGSDFTAEDVVFSLDRPATLTNSPGP-FTSYTKQIVGKEIVD 148 A D + F L +F++G +A DV +S D TL P + S + +VD Sbjct: 118 APDRMSMTFHLNPKARFNNGDKVSAADVKYSFD---TLMAKGAPQYKSVFADVKACVVVD 174 Query: 149 PYTVRLKTATPYGPLALDVSTIFIVSKKAAQNATTEDFNSGKALIGTGPFKFGNFERGDS 208 TVR A+ L L V+++ + S+K AQ T D I TGP+ ++ G S Sbjct: 175 ASTVRFDFASSNHELPLIVASVPVFSRKWAQ-GTPFDQIQLTPPISTGPYLIERYDTGRS 233 Query: 209 IELVRNDSYWG-------GKADWDKVTFRILTSDGARLAALLAGEVDAIDSVPPADVPKL 261 I RN YWG G +++++ +R D ARL A AGE D + + + Sbjct: 234 ITYKRNPDYWGKDVPARRGMFNFERIVYRFYKDDLARLEAFKAGEFDVVVEYSAKNWARS 293 Query: 262 KTNPKFSLVQRTSWRTIFWTLDQSRDKTPDITDKSG--KPLDKNPLKDIRVRQAISKAI- 318 T P+F R I + K + G L ++ KD+RVRQAI A+ Sbjct: 294 YTGPQFR-----DGRII-----KKEFKHSNGAGMQGFVMNLRRDQFKDVRVRQAIGLALD 343 Query: 319 ----NRQA-----------LTERTLEGLGTPASNIVA-------------PGILGYA--- 347 NRQ L G P + +A P + G A Sbjct: 344 YEWMNRQLFYGQYTRIYSFFNNSDLAATGEPQGDELALLKSLQAKGLKIDPAVFGPAPVP 403 Query: 348 ---DKLKVEKYDPEGAKKLLAEAG--YPNGFALTLHG-PNNRYINDE-----RVVQTVAQ 396 + + + A++LLA+AG Y +G G P + I D+ RV+ A+ Sbjct: 404 PSTNPPSSLRANLRQARELLAQAGWVYRDGAVRNAQGVPLSFEILDDQSSMSRVISVFAR 463 Query: 397 FLSRVGIQTKVETFPLSVYFGKARNGDFSVALLGW-GTLAGDFGLRTLVGTTDAATGWGS 455 L +GI + ++ + + DF + + + T + L + G+ AA GS Sbjct: 464 NLRTLGIDVVQRSADYALVAKRMEDFDFDMTSIRFPDTSSPGNELLDMFGSR-AADEKGS 522 Query: 456 WN-WGKYSNPQVDKLVQSSLSSVDEKQRQDFAQQAATVALNDYAVIPLHHQYAT 508 N WG +P VD+LVQ+ +++ + A+ V L+ Y V+P H Y++ Sbjct: 523 NNAWG-LKDPVVDQLVQTVIAADTRVKLTAAARALDRVLLHKYIVVP--HWYSS 573 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 0.317 0.134 0.399 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: 1,692,684 Number of extensions: 73220 Number of successful extensions: 241 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 220 Number of HSP's successfully gapped: 6 Length of query: 533 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 443 Effective length of database: 1,193,720 Effective search space: 528817960 Effective search space used: 528817960 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)