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= 0001.3501.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... 934 0.0 gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter perip... 110 3e-25 gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter perip... 84 4e-17 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 64 2e-11 >gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter periplasmic peptide-binding protein [Herbaspirillum seropedicae SmR1] Length = 540 Score = 934 bits (2415), Expect = 0.0, Method: Compositional matrix adjust. Identities = 442/539 (82%), Positives = 479/539 (88%) Query: 1 MSNQEKERFFSAEFTSIDDSGRGISDGFTRRDMMRTLMAGSLLTLSSTSLIAVSNSAMAQ 60 MS QE R + GF+RRDMMRTL+AGSL+T+ T L+ S S MAQ Sbjct: 1 MSKQENGRHPQEGSIITSHTLEHAQGGFSRRDMMRTLLAGSLMTVGGTGLLTASGSVMAQ 60 Query: 61 TPKRGGKLRIATQTSSTSDTLDPAKAAHATDYARVNLFYNGLTKLDSKLAPQMVLAEELL 120 T KRGGK+RIATQTSST+DTLDPAK AH+TDY RV++FYNGLTKLD KL PQMVLAEE+L Sbjct: 61 TGKRGGKMRIATQTSSTADTLDPAKTAHSTDYTRVHMFYNGLTKLDGKLGPQMVLAEEML 120 Query: 121 TSDAITWTVKLRRDVLFHDGKPFTPADVVYSLMRHKDPAVASKVKVVADQIESVKATGPN 180 T+DA+TWTVKLR+ V FHDGKP TPADVVYS+MRHKDPA ASKVKVVADQ ESVKATGPN Sbjct: 121 TNDAVTWTVKLRKGVNFHDGKPLTPADVVYSIMRHKDPATASKVKVVADQFESVKATGPN 180 Query: 181 EVQIKLSGANADFPVILSTAQFLIIRDGTTEFRTPNGTGAFKCKEFTPGVRTIAVRNENY 240 EVQIKL+ ANAD PVIL+TAQFLIIRDGTT F TPNGTGAFK KEFTPGVRTI VRNENY Sbjct: 181 EVQIKLTSANADLPVILATAQFLIIRDGTTNFSTPNGTGAFKLKEFTPGVRTIGVRNENY 240 Query: 241 WKSGMPYLDEVEVFGIPDEAARVNALLSGDVQWINDVNARSTERVRTTAGYTVMETKTGL 300 WK G+PYLDEVE+FGIPDEAARVNALLSGDV WINDVN+RST RV+ T GYTVMETK+G Sbjct: 241 WKPGLPYLDEVELFGIPDEAARVNALLSGDVHWINDVNSRSTGRVKNTPGYTVMETKSGQ 300 Query: 301 YTDLVIRQDVAPGNSMDFTLGMKYLIDREQIKTAAFRGYAVVANDQPIDPTNRFYFPGLP 360 YTDLV+RQDVAPGNSMDFTLGMKYL+DREQIK AAFRGYAV+ANDQPIDPTNRFYF GLP Sbjct: 301 YTDLVMRQDVAPGNSMDFTLGMKYLLDREQIKMAAFRGYAVIANDQPIDPTNRFYFAGLP 360 Query: 361 QRQYDPDKAKFYLQKAGVLGSTIPLVASVAATGSVDIAVLMQQSAQKIGLKLDVKRVPAD 420 QR YDPDKAKF+L KAGVLGSTIP+VASVAATGSVD+AVLMQQSA KIGLKLDVKRVPAD Sbjct: 361 QRPYDPDKAKFHLGKAGVLGSTIPIVASVAATGSVDMAVLMQQSAAKIGLKLDVKRVPAD 420 Query: 421 GYWSNQWMKVPLGFGNINPRPSADILFTQLFKSDAQWNESGWKNAQFDQLLVAARGETDF 480 GYWSNQWMKVP+GFGNINPRPSADIL TQ FKSDAQWNESGWKN QFDQL+VAARGETDF Sbjct: 421 GYWSNQWMKVPVGFGNINPRPSADILLTQFFKSDAQWNESGWKNPQFDQLVVAARGETDF 480 Query: 481 NKRKQMYADMQTLVHEKCGIGIPVFIVNLEGVSTKVKGITPVPLGAFMNYTCAEYVWLD 539 KRK MYAD+QT++HEKCG+GIPVFI+NLEG+STKVKGI PVPLGAFMNYTCAEYVWLD Sbjct: 481 TKRKAMYADLQTMIHEKCGLGIPVFIINLEGISTKVKGIDPVPLGAFMNYTCAEYVWLD 539 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 110 bits (275), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 138/490 (28%), Positives = 211/490 (43%), Gaps = 58/490 (11%) Query: 80 TLDPAKAAHATDYARVNLFYNGLTKLD-SKLAPQMVLAEELLTSDAITWTVKLRRDVLFH 138 +LDP HA D + F++ L + D +KL P + ++ + + D TW KLR +V + Sbjct: 41 SLDPQLNNHAGDRSVDLHFWDLLVQNDYNKLVPGLAVSWKNI--DPKTWEFKLRPNVKWQ 98 Query: 139 DGKPFTPADVVYSLMRHKDPAVASKVKVVAD---QIESVKATGPNEVQIKLSGANADFPV 195 DGKPFT DV++S R + AV V A +ESV A P + IK + N D P+ Sbjct: 99 DGKPFTADDVIFSYQRAR--AVPGSVATFAGYLRTVESVTAKDPLTLVIKTNIPNPDLPL 156 Query: 196 ILSTAQFL---IIRDGTTEFRTPN----GTGAFKCKEFTPGVRTIAVRNENYWKSGMPYL 248 L++ + I TTE GTG +K +TPG R + RN++YW +G P Sbjct: 157 NLASVHIVSKHIGEKSTTENYNSGAAVIGTGPYKFVSYTPGDRVVMQRNDDYW-NGKPLW 215 Query: 249 DEVEVFGIPDEAARVNALLSGDVQWINDVNARSTERVRTTAGYTVMETKTGLYTDLV--- 305 ++V I + AAR ALLSGDV I+ V+ +++ + V GL L+ Sbjct: 216 EKVNYRYINNGAARTAALLSGDVDVIDKVSVSDLAKLKQSPNVKVYPY-NGLRVLLIQPS 274 Query: 306 IRQDVAP------GNSMD--------FTLGMKYLIDREQIKTAAFRGYAVVANDQPIDPT 351 Q +P G +D M I+R+ + +G A AN P Sbjct: 275 FHQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKALIDRILQGAATEANQWM--PA 332 Query: 352 NRF-YFPGLPQRQYDPDKAKFYLQKAGVLGSTIPLVASVAATGSVDIAVLMQQSAQ---K 407 + F Y P + +D +AK L AG L V MQ AQ + Sbjct: 333 DTFGYNPEIKNIPFDAAQAKKLLADAG-FPDGFKLTIHVPNDRYPQAPETMQAVAQFWTR 391 Query: 408 IGLKLDVKRVPADGYWS----NQWMKVPLGFGNINPRPSADILFTQLFKSD-------AQ 456 IG+K V+ +P Y S N++ L +GN S L L D + Sbjct: 392 IGIKTQVEVLPWAAYSSRANKNEFAVSVLAWGNGTGEASY-ALVNVLGSVDPKKGIGASN 450 Query: 457 WNESGWKNAQFDQLLVAARGETDFNKRKQMYADMQTLVHEKCGIGIPVFIVNLEGVSTKV 516 WN + + D+ L + E D KR+ + V E+ G+ IP++ + + + Sbjct: 451 WNH--YSSPAVDKALADSTAEFDAAKREAILRGAAKTVSEEVGV-IPLY--HYQNIWAAK 505 Query: 517 KGITPVPLGA 526 KG+ P+ + Sbjct: 506 KGLKVTPISS 515 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 83.6 bits (205), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 112/474 (23%), Positives = 195/474 (41%), Gaps = 33/474 (6%) Query: 76 STSDTLDPAKAAHATDYARVNLFYNGLTKLDSKLAPQMVLAEELLTS-DAITWTVKLRRD 134 ST TLDP A + FY GL D + VLAE L S D + +T++L++ Sbjct: 44 STFTTLDPYDANDTLSLSMAKSFYQGLFGFDKDMKLIPVLAEGYLVSKDGLEYTIRLKQG 103 Query: 135 VLFHDGKPFTPADVVYSLM-RHKDPAVASKVKVVADQIESVKATGPNEVQIKLSGANADF 193 V F DG F AD V ++ R +P K + ++I + V++ L + F Sbjct: 104 VKFQDGTVFK-ADAVKAVFDRVTNPDNKLKRYNLFNRIAKTEILNDYTVKVVLKEPFSAF 162 Query: 194 PVILSTAQFLII------RDGTTEFR-TPNGTGAFKCKEFTPGVRTIAVRNENYWKSGMP 246 +L+ ++I + G + P GTG FK E+ + + YWK G P Sbjct: 163 INVLAHPSAVMISPTALKQYGNKDIAFHPVGTGPFKFVEWKQTDYVKVAKFDGYWKPGYP 222 Query: 247 YLDEVEVFGIPDEAARVNALLSGDVQWINDVNARSTERVRTTAGYTVMETKTGLYTDLVI 306 +DE+ + D AR + +G+ Q+ + + +++ + V+ + + + + Sbjct: 223 KVDEIIWKPVVDNNARSAMMQTGEAQFTYPLPYEQADLLKSKSNLDVVAAPSIIQRYMSM 282 Query: 307 RQDVAPGNSMDFTLGMKYLIDREQIKTAAFRGYAVVANDQPID---PTNRFYFPGLPQRQ 363 P ++ + Y I+++ + AF GYAV P+D P Y Sbjct: 283 NTKQKPFDNPKVREAINYAINKQALVKVAFNGYAV-----PMDGVVPQGVDYAYKTGPWP 337 Query: 364 YDPDKAKFYLQKAGVL-GSTIPLVASVAATGSVDIAVLMQQSAQKIGLKLDV------KR 416 YD KAK L +AG G L ++ + +V I +QQ ++G+K + +R Sbjct: 338 YDVKKAKALLAEAGYPNGFETELWSAYTHSTAVKIVQFLQQQLAQVGIKAKIQALEAGQR 397 Query: 417 VPADGYWSNQWMKVP---LGFGNINPRPSADILFTQLFKSDA----QWNESGWKNAQFDQ 469 V W + P L G + AD L S++ +N + +KN + D Sbjct: 398 VERVESWQDP-ATAPVRLLYIGWSSSTGEADWALRPLLASESFPPRLYNTAYYKNDKVDA 456 Query: 470 LLVAARGETDFNKRKQMYADMQTLVHEKCGIGIPVFIVNLEGVSTKVKGITPVP 523 + A T+ ++ +Y D Q + + V L + +KG+ +P Sbjct: 457 DIAKALTLTERKDKEALYKDAQQEIWKDAPWAFLVTEKLLYARNKNLKGVYVMP 510 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 59/220 (26%), Positives = 92/220 (41%), Gaps = 24/220 (10%) Query: 96 NLFYNGLTKLDSK---LAPQMVLAEELLTSDAITWTVKLRRDVLFHDGKPFTPADVVYSL 152 +L ++ L D K PQ+ A + + A+ + LR+ V F +G F+ DVV++ Sbjct: 62 HLIWDTLIYRDPKTNEYKPQLATAWKWESPTALV--LDLRQGVQFQNGDKFSADDVVFTF 119 Query: 153 MRHKDPAVASKVKVVADQIESVKATGPNEVQIKLSGANADFPV----------ILSTAQF 202 P + + D I+SV +V+I L G FP I A F Sbjct: 120 NYAVSPESKAVTRQNTDWIKSVDKLADYKVRINLKGP---FPAALEYLAGPLPIYPAAYF 176 Query: 203 LIIRDGTTEF-RTPNGTGAFKCKEFTPGVRTIAVRNENYWK---SGMPYLDEVEVFGIPD 258 + G F + P GTG +K TPG V+N Y+K G P + ++ IPD Sbjct: 177 KKV--GLEGFSKAPIGTGPYKVTSVTPGQGVTLVKNPGYFKDSPQGQPTIGNIKFVVIPD 234 Query: 259 EAARVNALLSGDVQWINDVNARSTERVRTTAGYTVMETKT 298 R L++G + WI V + ++T V +T Sbjct: 235 PETRAAQLMTGAIDWIWRVPPDQADSLKTNPKLAVQSGET 274 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 0.389 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: 1,669,952 Number of extensions: 69311 Number of successful extensions: 193 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 189 Number of HSP's successfully gapped: 4 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)