Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 313 bits (803), Expect = 7e-90 Identities = 173/479 (36%), Positives = 282/479 (58%), Gaps = 7/479 (1%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 +LQ + K +AG+ LRD +L+L G +HAL G NGAGKST + +L G+ + G + L Sbjct: 18 VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPR---RAGCIVDNKALNR 122 G V + P A GI+ + QE+ P ++VAENI+ GR PR G +D L++ Sbjct: 78 GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQ 137 Query: 123 RTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTL 182 R R+L+ + +D T + VA QLV IA+A S + +V+I+DEPTS++ + E Q L Sbjct: 138 RARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQKL 197 Query: 183 FKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQ 242 F+ +RRL ++G IV+V+H L+++ ++D ++ R+G++V D+ L+ ++G+ Sbjct: 198 FEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLGR 257 Query: 243 ELTRIDHKVGRECAANT----CLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEF 298 +L + A ++ LQ + L + + + LQ+R GE++G+ GL+GSGR+E Sbjct: 258 DLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRTEL 317 Query: 299 LNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALS 358 ++GL D G++ + G+ + P I G++L E+RK G+V S+ NIAL+ Sbjct: 318 ARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIALA 377 Query: 359 AYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPV 418 R+ ++ ++T+LAE VK L IKT +++ P+ +SGGNQQK +LA+ ++ EP Sbjct: 378 LQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIEPR 437 Query: 419 CLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV 477 L+ DEPTRGID AKQEI + + + G A + +SSE E++ ++ RI V + R V Sbjct: 438 LLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRKV 496 Lambda K H 0.319 0.135 0.381 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: 564 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 495 Length of database: 517 Length adjustment: 34 Effective length of query: 461 Effective length of database: 483 Effective search space: 222663 Effective search space used: 222663 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