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= 0001.3939.p (540 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter perip... 945 0.0 gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter perip... 110 2e-25 gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter perip... 83 6e-17 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 61 2e-10 >gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter periplasmic peptide-binding protein [Herbaspirillum seropedicae SmR1] Length = 540 Score = 945 bits (2443), Expect = 0.0, Method: Compositional matrix adjust. Identities = 448/540 (82%), Positives = 486/540 (90%) Query: 1 MSNQENERFFSDEFTGAAESGSGIREGFTRRDMMRTLMAGSLLTLGSTSLMAVSSSAMAQ 60 MS QEN R + + + + GF+RRDMMRTL+AGSL+T+G T L+ S S MAQ Sbjct: 1 MSKQENGRHPQEGSIITSHTLEHAQGGFSRRDMMRTLLAGSLMTVGGTGLLTASGSVMAQ 60 Query: 61 TPKRGGKLRMATQTSSTADTLDPAKAAHATDYTRVNLFYNGLTKLDSKLGPQMVLAEELL 120 T KRGGK+R+ATQTSSTADTLDPAK AH+TDYTRV++FYNGLTKLD KLGPQMVLAEE+L Sbjct: 61 TGKRGGKMRIATQTSSTADTLDPAKTAHSTDYTRVHMFYNGLTKLDGKLGPQMVLAEEML 120 Query: 121 TTDAITWTVKLRKDVIFHDGKPFTPADVVYSLMRHKDPAVASKVKVVADQIESVKATGPN 180 T DA+TWTVKLRK V FHDGKP TPADVVYS+MRHKDPA ASKVKVVADQ ESVKATGPN Sbjct: 121 TNDAVTWTVKLRKGVNFHDGKPLTPADVVYSIMRHKDPATASKVKVVADQFESVKATGPN 180 Query: 181 EVQIKLAGANADLPVILSTAQFLIIRDGTTEFRTPNGTGAFKCKEFTPGVRTIGVRNENY 240 EVQIKL ANADLPVIL+TAQFLIIRDGTT F TPNGTGAFK KEFTPGVRTIGVRNENY Sbjct: 181 EVQIKLTSANADLPVILATAQFLIIRDGTTNFSTPNGTGAFKLKEFTPGVRTIGVRNENY 240 Query: 241 WKSGMPYLDEVEVFGIPDEAARVNALLSGDVHWINDVNARSTERVRTSAGYTVIETRTGL 300 WK G+PYLDEVE+FGIPDEAARVNALLSGDVHWINDVN+RST RV+ + GYTV+ET++G Sbjct: 241 WKPGLPYLDEVELFGIPDEAARVNALLSGDVHWINDVNSRSTGRVKNTPGYTVMETKSGQ 300 Query: 301 YTDLVIRQDVAPGNSMDFTLGMKYLMDREQIKNAAFRGYAVTANDQPIDPTNRFYFPGLP 360 YTDLV+RQDVAPGNSMDFTLGMKYL+DREQIK AAFRGYAV ANDQPIDPTNRFYF GLP Sbjct: 301 YTDLVMRQDVAPGNSMDFTLGMKYLLDREQIKMAAFRGYAVIANDQPIDPTNRFYFAGLP 360 Query: 361 QRPYDPDKAKFHLQKAGVLGSTIPLVASAAATGSVDIAVLMQQSAQKIGLKLDVKRVPPD 420 QRPYDPDKAKFHL KAGVLGSTIP+VAS AATGSVD+AVLMQQSA KIGLKLDVKRVP D Sbjct: 361 QRPYDPDKAKFHLGKAGVLGSTIPIVASVAATGSVDMAVLMQQSAAKIGLKLDVKRVPAD 420 Query: 421 GYWSNQWMKVPLGFGNINPRPSADILFTQLFKSDAQWNESGWKNAQFDQLLVAARGETDF 480 GYWSNQWMKVP+GFGNINPRPSADIL TQ FKSDAQWNESGWKN QFDQL+VAARGETDF Sbjct: 421 GYWSNQWMKVPVGFGNINPRPSADILLTQFFKSDAQWNESGWKNPQFDQLVVAARGETDF 480 Query: 481 NKRKQMYADMQTLVHEKCGIGIPVFIINLEGVNTKVKGITPVPLGAFMNYTCAEYVWLDA 540 KRK MYAD+QT++HEKCG+GIPVFIINLEG++TKVKGI PVPLGAFMNYTCAEYVWLDA Sbjct: 481 TKRKAMYADLQTMIHEKCGLGIPVFIINLEGISTKVKGIDPVPLGAFMNYTCAEYVWLDA 540 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 110 bits (276), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 140/495 (28%), Positives = 207/495 (41%), Gaps = 68/495 (13%) Query: 80 TLDPAKAAHATDYTRVNLFYNGLTKLD-SKLGPQMVLAEELLTTDAITWTVKLRKDVIFH 138 +LDP HA D + F++ L + D +KL P + ++ + D TW KLR +V + Sbjct: 41 SLDPQLNNHAGDRSVDLHFWDLLVQNDYNKLVPGLAVSWK--NIDPKTWEFKLRPNVKWQ 98 Query: 139 DGKPFTPADVVYSLMRHKDPAVASKVKVVAD---QIESVKATGPNEVQIKLAGANADLPV 195 DGKPFT DV++S R + AV V A +ESV A P + IK N DLP+ Sbjct: 99 DGKPFTADDVIFSYQRAR--AVPGSVATFAGYLRTVESVTAKDPLTLVIKTNIPNPDLPL 156 Query: 196 ILSTAQFL---IIRDGTTEFRTPN----GTGAFKCKEFTPGVRTIGVRNENYWKSGMPYL 248 L++ + I TTE GTG +K +TPG R + RN++YW +G P Sbjct: 157 NLASVHIVSKHIGEKSTTENYNSGAAVIGTGPYKFVSYTPGDRVVMQRNDDYW-NGKPLW 215 Query: 249 DEVEVFGIPDEAARVNALLSGDVHWINDVNARSTERVRTSAGYTV--------------- 293 ++V I + AAR ALLSGDV I+ V+ +++ S V Sbjct: 216 EKVNYRYINNGAARTAALLSGDVDVIDKVSVSDLAKLKQSPNVKVYPYNGLRVLLIQPSF 275 Query: 294 -------IETRTGLYTDLVIRQDVAPGNSMDFTLGMKYLMDREQIKNAAFRGYAVTANDQ 346 I G D DV +M + K L+DR +G A AN Sbjct: 276 HQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKALIDR------ILQGAATEANQW 329 Query: 347 PIDPTNRF-YFPGLPQRPYDPDKAKFHLQKAGVLGSTIPLVASAAATGSVDIAVLMQQSA 405 P + F Y P + P+D +AK L AG L MQ A Sbjct: 330 M--PADTFGYNPEIKNIPFDAAQAKKLLADAG-FPDGFKLTIHVPNDRYPQAPETMQAVA 386 Query: 406 Q---KIGLKLDVKRVPPDGYWS----NQWMKVPLGFGNINPRPSADILFTQLFKSD---- 454 Q +IG+K V+ +P Y S N++ L +GN S L L D Sbjct: 387 QFWTRIGIKTQVEVLPWAAYSSRANKNEFAVSVLAWGNGTGEASY-ALVNVLGSVDPKKG 445 Query: 455 ---AQWNESGWKNAQFDQLLVAARGETDFNKRKQMYADMQTLVHEKCGIGIPVFIINLEG 511 + WN + + D+ L + E D KR+ + V E+ G+ IP++ + + Sbjct: 446 IGASNWNH--YSSPAVDKALADSTAEFDAAKREAILRGAAKTVSEEVGV-IPLY--HYQN 500 Query: 512 VNTKVKGITPVPLGA 526 + KG+ P+ + Sbjct: 501 IWAAKKGLKVTPISS 515 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 82.8 bits (203), Expect = 6e-17, Method: Compositional matrix adjust. Identities = 110/474 (23%), Positives = 195/474 (41%), Gaps = 33/474 (6%) Query: 76 STADTLDPAKAAHATDYTRVNLFYNGLTKLDSKLGPQMVLAE-ELLTTDAITWTVKLRKD 134 ST TLDP A + FY GL D + VLAE L++ D + +T++L++ Sbjct: 44 STFTTLDPYDANDTLSLSMAKSFYQGLFGFDKDMKLIPVLAEGYLVSKDGLEYTIRLKQG 103 Query: 135 VIFHDGKPFTPADVVYSLM-RHKDPAVASKVKVVADQIESVKATGPNEVQIKLAGA-NAD 192 V F DG F AD V ++ R +P K + ++I + V++ L +A Sbjct: 104 VKFQDGTVFK-ADAVKAVFDRVTNPDNKLKRYNLFNRIAKTEILNDYTVKVVLKEPFSAF 162 Query: 193 LPVILSTAQFLIIRDGTTEFRT------PNGTGAFKCKEFTPGVRTIGVRNENYWKSGMP 246 + V+ + +I ++ P GTG FK E+ + + YWK G P Sbjct: 163 INVLAHPSAVMISPTALKQYGNKDIAFHPVGTGPFKFVEWKQTDYVKVAKFDGYWKPGYP 222 Query: 247 YLDEVEVFGIPDEAARVNALLSGDVHWINDVNARSTERVRTSAGYTVIETRTGLYTDLVI 306 +DE+ + D AR + +G+ + + + +++ + V+ + + + + Sbjct: 223 KVDEIIWKPVVDNNARSAMMQTGEAQFTYPLPYEQADLLKSKSNLDVVAAPSIIQRYMSM 282 Query: 307 RQDVAPGNSMDFTLGMKYLMDREQIKNAAFRGYAVTANDQPID---PTNRFYFPGLPQRP 363 P ++ + Y ++++ + AF GYAV P+D P Y P Sbjct: 283 NTKQKPFDNPKVREAINYAINKQALVKVAFNGYAV-----PMDGVVPQGVDYAYKTGPWP 337 Query: 364 YDPDKAKFHLQKAGVL-GSTIPLVASAAATGSVDIAVLMQQSAQKIGLKLDV------KR 416 YD KAK L +AG G L ++ + +V I +QQ ++G+K + +R Sbjct: 338 YDVKKAKALLAEAGYPNGFETELWSAYTHSTAVKIVQFLQQQLAQVGIKAKIQALEAGQR 397 Query: 417 VPPDGYWSNQWMKVP---LGFGNINPRPSADILFTQLFKSDA----QWNESGWKNAQFDQ 469 V W + P L G + AD L S++ +N + +KN + D Sbjct: 398 VERVESWQDP-ATAPVRLLYIGWSSSTGEADWALRPLLASESFPPRLYNTAYYKNDKVDA 456 Query: 470 LLVAARGETDFNKRKQMYADMQTLVHEKCGIGIPVFIINLEGVNTKVKGITPVP 523 + A T+ ++ +Y D Q + + V L N +KG+ +P Sbjct: 457 DIAKALTLTERKDKEALYKDAQQEIWKDAPWAFLVTEKLLYARNKNLKGVYVMP 510 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 57/208 (27%), Positives = 90/208 (43%), Gaps = 20/208 (9%) Query: 96 NLFYNGLTKLDSKLG---PQMVLAEELLTTDAITWTVKLRKDVIFHDGKPFTPADVVYSL 152 +L ++ L D K PQ+ A + + A+ + LR+ V F +G F+ DVV++ Sbjct: 62 HLIWDTLIYRDPKTNEYKPQLATAWKWESPTALV--LDLRQGVQFQNGDKFSADDVVFTF 119 Query: 153 MRHKDPAVASKVKVVADQIESVKATGPNEVQIKLAGA--------NADLPVILSTAQFLI 204 P + + D I+SV +V+I L G LP I A F Sbjct: 120 NYAVSPESKAVTRQNTDWIKSVDKLADYKVRINLKGPFPAALEYLAGPLP-IYPAAYFKK 178 Query: 205 IRDGTTEF-RTPNGTGAFKCKEFTPGVRTIGVRNENYWK---SGMPYLDEVEVFGIPDEA 260 + G F + P GTG +K TPG V+N Y+K G P + ++ IPD Sbjct: 179 V--GLEGFSKAPIGTGPYKVTSVTPGQGVTLVKNPGYFKDSPQGQPTIGNIKFVVIPDPE 236 Query: 261 ARVNALLSGDVHWINDVNARSTERVRTS 288 R L++G + WI V + ++T+ Sbjct: 237 TRAAQLMTGAIDWIWRVPPDQADSLKTN 264 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 0.133 0.393 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: 1,673,152 Number of extensions: 69406 Number of successful extensions: 197 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 195 Number of HSP's successfully gapped: 5 Length of query: 540 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 450 Effective length of database: 1,193,720 Effective search space: 537174000 Effective search space used: 537174000 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)