Align ABC transporter related (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 453 bits (1165), Expect = e-132 Identities = 242/484 (50%), Positives = 334/484 (69%), Gaps = 7/484 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 +L+L I K + G+ L DV L L+ GE+HAL+G+NGAGKSTL+KV+TG G + Sbjct: 18 VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGL-----IHFKKMY 118 G+ ++P+ AQ+ GISTVYQEVNL PNL+VA+N+F G PR G+ I + ++ Sbjct: 78 GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPR-CGIAQGFRIDWATLH 136 Query: 119 ADARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQV 178 AR ++ + L IDV+ LSDY +AVQQL+AIAR +++ ++VL+LDEPT+SLD EVQ Sbjct: 137 QRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQK 196 Query: 179 LFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238 LF +L +L+++G++IVF+THFL+QVY +SDRITVLRNG ++GE+L +L LI AMLG Sbjct: 197 LFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLG 256 Query: 239 RSLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRS 298 R L ++ V A LL E + +Q ++L + G+ VGLAGLLGSGR+ Sbjct: 257 RDLAAAS-EQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRT 315 Query: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358 E+ +FGL+ D G++ + GQ + + P+DAI G+ALCPE+RK DGI+ LS+RENI Sbjct: 316 ELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIA 375 Query: 359 LALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418 LALQAR+G ++LS + Q E+A+ ++ L I T DKPI LSGGNQQK ILARW+AIE Sbjct: 376 LALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIE 435 Query: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478 P LL+LDEPTRGID+ A EI+ I L GM++L SSE+ E+V ++++VVLRDR Sbjct: 436 PRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRK 495 Query: 479 VREL 482 V EL Sbjct: 496 VGEL 499 Score = 72.8 bits (177), Expect = 3e-17 Identities = 62/237 (26%), Positives = 111/237 (46%), Gaps = 30/237 (12%) Query: 274 IQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISA 333 ++ + L + G+ L G G+G+S + + G+ G + L GQ + P+ A Sbjct: 34 LRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRL 93 Query: 334 GIA-------LCPEDRKIDGIIGPLSIRENIILALQARIGW-------WRYLSNTRQQEI 379 GI+ LCP LS+ ENI R G W L + + Sbjct: 94 GISTVYQEVNLCPN----------LSVAENIFAGRYPRCGIAQGFRIDWATLHQRARDLV 143 Query: 380 AQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEI 439 A+ + ++ + +D P+ QQ V +AR L+IE +L+LDEPT +D ++ Sbjct: 144 ARIGL-QIDVTRLLSDYPVAV-----QQLVAIARALSIESRVLILDEPTSSLDDDEVQKL 197 Query: 440 VKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQAI 496 +++R L EG+S++ + L+++ A S+++ VLR+ V E +L Q ++ A+ Sbjct: 198 FEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAM 254 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: 701 Number of extensions: 26 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: 517 Length adjustment: 34 Effective length of query: 465 Effective length of database: 483 Effective search space: 224595 Effective search space used: 224595 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