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= 0001.4600.p (550 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... 139 6e-34 gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter perip... 108 8e-25 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 97 3e-21 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 139 bits (350), Expect = 6e-34, Method: Compositional matrix adjust. Identities = 138/474 (29%), Positives = 214/474 (45%), Gaps = 57/474 (12%) Query: 68 WNLSKADKASELIADLALSWQ-VEPKDKTKWIFKLRPGVKFHDGSPFNADAVVWNVNKVL 126 W+L + ++L+ LA+SW+ ++PK W FKLRP VK+ DG PF AD V+++ + Sbjct: 60 WDLLVQNDYNKLVPGLAVSWKNIDPK---TWEFKLRPNVKWQDGKPFTADDVIFSYQRA- 115 Query: 127 DKNAVQFDPSQVGVTASRMPTLRSARKIDDLTVELTTSEPDSFLPINLTNLFMASPSQWE 186 AV P V A + T+ S D LT+ + T+ P+ LP+NL ++ + S E Sbjct: 116 --RAV---PGSVATFAGYLRTVESVTAKDPLTLVIKTNIPNPDLPLNLASVHIVSKHIGE 170 Query: 187 KKLAAVPASVTDKAERSKQAWAAFAADASGTGPFKMAKFVPRERLEVVKNDGYWDPARRP 246 K S T+ A GTGP+K + P +R+ + +ND YW+ +P Sbjct: 171 K-------STTENYNS--------GAAVIGTGPYKFVSYTPGDRVVMQRNDDYWN--GKP 213 Query: 247 KIDRVVMLPLPEANSRTAALMSGQVDWIEAPAPDALDAIKAR-GFKIYSNPQPHVWPWQL 305 ++V + +RTAAL+SG VD I+ + L +K K+Y V Q Sbjct: 214 LWEKVNYRYINNGAARTAALLSGDVDVIDKVSVSDLAKLKQSPNVKVYPYNGLRVLLIQP 273 Query: 306 SFLPG---------------SPWLDKRVRHAANLCVNRPAM-KQLLGGLMGEATGTVEPG 349 SF G +P LD RVR A +L +NR A+ ++L G EA + P Sbjct: 274 SFHQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKALIDRILQGAATEANQWM-PA 332 Query: 350 HPWRGNPSFQ-IKYDPAAAKKLMTEAGYSAAKPLTVKVQISASGSGQMQPLPMNEFMQQN 408 + NP + I +D A AKKL+ +AG+ P K+ I Q + + Q Sbjct: 333 DTFGYNPEIKNIPFDAAQAKKLLADAGF----PDGFKLTIHVPNDRYPQAPETMQAVAQF 388 Query: 409 LKECFFDVQFDVIEWNTLYT--NWRIGAKDPSAHGANAINVSFASMDPFFAMVRFVDTKA 466 Q +V+ W + N A A G S+A ++ ++ VD K Sbjct: 389 WTRIGIKTQVEVLPWAAYSSRANKNEFAVSVLAWGNGTGEASYALVN----VLGSVDPKK 444 Query: 467 APPTSNNWGFYSNPEVDALIAKARTTFDPKQRDALLAQLHAKIVDEAPFVWVAH 520 S NW YS+P VD +A + FD +R+A+L + +E + + H Sbjct: 445 GIGAS-NWNHYSSPAVDKALADSTAEFDAAKREAILRGAAKTVSEEVGVIPLYH 497 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 108 bits (271), Expect = 8e-25, Method: Compositional matrix adjust. Identities = 126/496 (25%), Positives = 220/496 (44%), Gaps = 52/496 (10%) Query: 56 FTGIPMYDGLTQWNLSKA----------DKASELIADLALSWQVEPKDKTKWIFKLRPGV 105 FT + YD +LS A DK +LI LA + V KD ++ +L+ GV Sbjct: 46 FTTLDPYDANDTLSLSMAKSFYQGLFGFDKDMKLIPVLAEGYLVS-KDGLEYTIRLKQGV 104 Query: 106 KFHDGSPFNADAVVWNVNKVLDKNAVQFDPSQVGVTASRMPTLRSARKIDDLTVELTTSE 165 KF DG+ F ADAV V D+ +P + + ++D TV++ E Sbjct: 105 KFQDGTVFKADAV----KAVFDRVT---NPDNKLKRYNLFNRIAKTEILNDYTVKVVLKE 157 Query: 166 PDSFLPINLTNLFMASPSQWEKKLAAVPASVTDKAERSKQAWAAFAADASGTGPFKMAKF 225 P S IN+ +A PS + P ++ + A GTGPFK ++ Sbjct: 158 PFSAF-INV----LAHPSA----VMISPTALKQYGNKD------IAFHPVGTGPFKFVEW 202 Query: 226 VPRERLEVVKNDGYWDPARRPKIDRVVMLPLPEANSRTAALMSGQVDWIEAPAPDALDAI 285 + ++V K DGYW P PK+D ++ P+ + N+R+A + +G+ + + D + Sbjct: 203 KQTDYVKVAKFDGYWKPGY-PKVDEIIWKPVVDNNARSAMMQTGEAQFTYPLPYEQADLL 261 Query: 286 KARGFKIYSNPQPHVWPWQLSF-LPGSPWLDKRVRHAANLCVNRPAM-KQLLGGLMGEAT 343 K++ + P + +S P+ + +VR A N +N+ A+ K G Sbjct: 262 KSKS-NLDVVAAPSIIQRYMSMNTKQKPFDNPKVREAINYAINKQALVKVAFNGYAVPMD 320 Query: 344 GTVEPG--HPWRGNPSFQIKYDPAAAKKLMTEAGYSAAKPLTVKVQISASGSGQMQPLPM 401 G V G + ++ P YD AK L+ EAGY P + ++ S + + Sbjct: 321 GVVPQGVDYAYKTGP---WPYDVKKAKALLAEAGY----PNGFETEL-WSAYTHSTAVKI 372 Query: 402 NEFMQQNLKECFFDVQFDVIEWNTLYTNWRIGA-KDPSAHGANAINVSFASM--DPFFAM 458 +F+QQ L + + +E R+ + +DP+ + + ++S + +A+ Sbjct: 373 VQFLQQQLAQVGIKAKIQALEAGQRVE--RVESWQDPATAPVRLLYIGWSSSTGEADWAL 430 Query: 459 VRFVDTKAAPPTSNNWGFYSNPEVDALIAKARTTFDPKQRDALLAQLHAKIVDEAPFVWV 518 + +++ PP N +Y N +VDA IAKA T + K ++AL +I +AP+ ++ Sbjct: 431 RPLLASESFPPRLYNTAYYKNDKVDADIAKALTLTERKDKEALYKDAQQEIWKDAPWAFL 490 Query: 519 AHDTGPRAISAKVKGV 534 + A + +KGV Sbjct: 491 VTEKLLYARNKNLKGV 506 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 97.4 bits (241), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 116/455 (25%), Positives = 183/455 (40%), Gaps = 68/455 (14%) Query: 75 KASELIADLALSWQVEPKDKTKWIFKLRPGVKFHDGSPFNADAVVWNVNKVLDKNAVQFD 134 K +E LA +W+ E T + LR GV+F +G F+AD VV+ N + Sbjct: 74 KTNEYKPQLATAWKWE--SPTALVLDLRQGVQFQNGDKFSADDVVFTFNYAVS------- 124 Query: 135 PSQVGVTASRMPTLRSARKIDDLTVELTTSEPDSFLPINLTNLFMASPSQWEKKLAAVPA 194 P VT ++S K+ D V INL F A+ L PA Sbjct: 125 PESKAVTRQNTDWIKSVDKLADYKVR-----------INLKGPFPAALEYLAGPLPIYPA 173 Query: 195 SVTDKAERSKQAWAAFAADASGTGPFKMAKFVPRERLEVVKNDGYW--DPARRPKIDRVV 252 + K F+ GTGP+K+ P + + +VKN GY+ P +P I + Sbjct: 174 AYFKKV-----GLEGFSKAPIGTGPYKVTSVTPGQGVTLVKNPGYFKDSPQGQPTIGNIK 228 Query: 253 MLPLPEANSRTAALMSGQVDWIEAPAPDALDAIKARGFKIYSNPQPHVWPWQ---LSFL- 308 + +P+ +R A LM+G +DWI PD D++K +NP+ V + + F+ Sbjct: 229 FVVIPDPETRAAQLMTGAIDWIWRVPPDQADSLK-------TNPKLAVQSGETMRIGFIT 281 Query: 309 --------PGSPWLDKRVRHAANLCVNRPAMKQLL--GGLMGEATGTVEPGHPWRGNPSF 358 P SP+ D RVR A N +NR L GG T N + Sbjct: 282 LDTTGTSAPNSPFKDVRVRQAVNHAINRKGYADNLMRGGSQPVYTACFRTQFGCDSNAAI 341 Query: 359 QIKYDPAAAKKLMTEAGYSAAKPLTVKVQISASGSGQMQPLPMNEFMQQNLKECFFDVQF 418 + Y+PA AK+L+ AGY P I A + + E + +L++ + Sbjct: 342 KYDYNPAKAKELLAAAGY----PNGFDTDIYA-----YREREIAEAIIGDLRKVGIRARL 392 Query: 419 DVIEWNTLYTNWRIGAKDPSAHGANAINVSFASMDPFFAMVRFVDTKAAPPTSNNWGFYS 478 +++ L T +R G S + + +++ S FA V F Sbjct: 393 HYMKFAALQTEYRSGKTPMSFYSWGSFSMNDTSA---FAGVYF--------KGGADDITK 441 Query: 479 NPEVDALIAKARTTFDPKQRDALLAQLHAKIVDEA 513 +P++ + A T+ DP R A ++ I +A Sbjct: 442 DPQLQQYLQTADTSIDPAVRKANYSKAQELISKQA 476 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 0.132 0.412 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: 1,829,434 Number of extensions: 78198 Number of successful extensions: 235 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 223 Number of HSP's successfully gapped: 3 Length of query: 550 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 460 Effective length of database: 1,193,720 Effective search space: 549111200 Effective search space used: 549111200 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 (21.8 bits) S2: 133 (55.8 bits)