Align ABC transporter related (characterized, see rationale)
to candidate SM_b20507 SM_b20507 L-arabinose transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Smeli:SM_b20507 Length = 508 Score = 352 bits (904), Expect = e-101 Identities = 187/497 (37%), Positives = 314/497 (63%), Gaps = 8/497 (1%) Query: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 M LE + ISK YPGV+AL +VS + G VH L+GENGAGKSTL++V++G Q+ D G+ Sbjct: 1 MQDFLEFQSISKGYPGVQALSEVSFSVRKGAVHGLMGENGAGKSTLIRVLSGDQAADTGE 60 Query: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120 I GEPQH+ + DA AG+ ++QE+ LVP LTVA+NL+LG P + G+I +++ Sbjct: 61 IRINGEPQHYRSVRDAFNAGVIVIHQELQLVPELTVAENLWLGRFPGKAGVIDRRQLIRV 120 Query: 121 ARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF 180 L + +D+D A ++ SI +Q++ IA+ V A+V+ LDEPT+SL ++E ++LF Sbjct: 121 VSDRLAEIGIDVDPEAKVASLSIGERQMVEIAKAVMTDARVIALDEPTSSLSSRESEILF 180 Query: 181 GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYL-TAELPQPKLIEAMLGR 239 ++++L++ G I++++H LD+++++ + +TVLR+G+ + +++ + ++I M+GR Sbjct: 181 ALIDRLRSNGTVILYVSHRLDEIFRLCNSLTVLRDGRLAAHHPDISKVGREQIIAEMVGR 240 Query: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSE 299 + + RT+ A L++E VS Q ++ TV G+ +G GL+G+GRSE Sbjct: 241 EISNIW---GWRARTLGAAR---LTVERVSGANLPQPISFTVRAGEILGFFGLIGAGRSE 294 Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359 + V+G D G + + G + P +I AG+ LCPEDRK DGI+ SI EN+ + Sbjct: 295 MARLVYGADRRRQGKVLVDGLAVPADSPRLSIRAGVVLCPEDRKFDGIVQGRSIEENMAI 354 Query: 360 ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEP 419 + + + + ++ E+A+ FI KL++ TP + I LSGGNQQKVIL RWL+ E Sbjct: 355 SSRRHFSPFGVVDKGKEAELAERFIAKLRVRTPSRHQDIVNLSGGNQQKVILGRWLSEEG 414 Query: 420 I-LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478 + +L++DEPTRGID+GA +EI +++ L +GM+++V SSEL E++ +++++V+ + Sbjct: 415 VKVLLIDEPTRGIDVGAKSEIYEILYELAAQGMAIVVISSELPEVMGIADRILVMCEGRI 474 Query: 479 VRELSGAELTSQHVMQA 495 E+ ++ ++ A Sbjct: 475 AAEIDRSDFDEHRILAA 491 Score = 68.6 bits (166), Expect = 5e-16 Identities = 59/232 (25%), Positives = 111/232 (47%), Gaps = 13/232 (5%) Query: 16 GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMD 75 G + +S + AGE+ G GAG+S + +++ GA + G +L G ++P Sbjct: 265 GANLPQPISFTVRAGEILGFFGLIGAGRSEMARLVYGADRRRQGKVLVDGLAVPADSPRL 324 Query: 76 AQKAGISTVYQEVN---LVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQ-FKLD 131 + +AG+ ++ +V ++ +N+ + R F + A L + F Sbjct: 325 SIRAGVVLCPEDRKFDGIVQGRSIEENMAIS---SRRHFSPFGVVDKGKEAELAERFIAK 381 Query: 132 IDVSAP-----LSDYSIAVQQLIAIARGVAMSA-KVLVLDEPTASLDAKEVQVLFGILNQ 185 + V P + + S QQ + + R ++ KVL++DEPT +D ++ IL + Sbjct: 382 LRVRTPSRHQDIVNLSGGNQQKVILGRWLSEEGVKVLLIDEPTRGIDVGAKSEIYEILYE 441 Query: 186 LKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAML 237 L A+G+AIV I+ L +V I+DRI V+ G+ E ++ + +++ A L Sbjct: 442 LAAQGMAIVVISSELPEVMGIADRILVMCEGRIAAEIDRSDFDEHRILAAAL 493 Lambda K H 0.319 0.136 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 633 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 499 Length of database: 508 Length adjustment: 34 Effective length of query: 465 Effective length of database: 474 Effective search space: 220410 Effective search space used: 220410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory