Align ABC transporter related (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 360 bits (924), Expect = e-104 Identities = 188/494 (38%), Positives = 309/494 (62%), Gaps = 7/494 (1%) Query: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64 L L I+K +PGVKAL DVSL L+ G+V AL+GENGAGKST+VK++TG D G IL Sbjct: 21 LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80 Query: 65 GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR-RLGLIHFKKMYADARA 123 G+P F+TP A G++ ++QE L L+VA+N+FLG+ PR GLI +KK +ARA Sbjct: 81 GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARA 140 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 +LT ++D L D IA + L+AIAR +++ A+V+++DEPTA+L KE++ L+ ++ Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 LKA+G AI+FI+H D++++I+D TV R+GQ IG+ A++ + L++ M+GR + + Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 + +L+++ + ++ T+ +G+ +G GL+G+GRSE + Sbjct: 261 IFPQR------APNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQS 314 Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363 +FG+ +GS+ + G + +S P DA+ GI PEDR G I L I +N+ L Sbjct: 315 LFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLG 374 Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423 RI +L + +A+ + ++L + D + LSGGNQQKV++A+WLA P +++ Sbjct: 375 RISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVII 434 Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483 LDEPT+G+DIG+ A + + L +G+++++ SSE+ E++ S++V+V+R+ V EL+ Sbjct: 435 LDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELA 494 Query: 484 GAELTSQHVMQAIA 497 G +L + +++ A Sbjct: 495 GDDLQPETLVRHAA 508 Score = 81.6 bits (200), Expect = 6e-20 Identities = 58/224 (25%), Positives = 106/224 (47%), Gaps = 6/224 (2%) Query: 21 EDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAG 80 +D+S L GE+ G GAG+S ++ + G G + G ++P DA G Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHG 345 Query: 81 ISTVYQE---VNLVPNLTVAQNLFLGYEPR--RLGLIHFKKMYADARAVLTQFKLDI-DV 134 I V ++ + +L + QN+ L R R G + + +A AR + L + Sbjct: 346 IVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASL 405 Query: 135 SAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKGVAIV 194 + + S QQ + IA+ +A +V++LDEPT +D + + +L A+G+A++ Sbjct: 406 DTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVI 465 Query: 195 FITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238 ++ + +V +SDR+ V+R G+ + E +L L+ G Sbjct: 466 MVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509 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: 584 Number of extensions: 37 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: 510 Length adjustment: 34 Effective length of query: 465 Effective length of database: 476 Effective search space: 221340 Effective search space used: 221340 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