Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 349 bits (896), Expect = e-100 Identities = 192/477 (40%), Positives = 302/477 (63%), Gaps = 10/477 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L+ GI K+F G+ + +V +Y EI +L+G+NGAGKSTLIK+LTGVL+ G++ + Sbjct: 18 VLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRL 77 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G+ V SP+ A + GIS ++QE+NLC N++VAENIF G + R+D + Sbjct: 78 GGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGF--RIDWATL 135 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + R+++L+ IG + L+ + A +Q+V I +AL E R++ +DEPTSSL +E + Sbjct: 136 HQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 +LFE++ L+S G+S+VFV+H L++V +SDRI V+R+G +GE + +I M+ Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255 Query: 254 GREVEFFPH------GIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGR 307 GR++ +++R + L+ L +++ + ++R GEV+G AGL+G+GR Sbjct: 256 GRDLAAASEQPAPAPAVDSRHANL-LQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGR 314 Query: 308 TETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNI 367 TE L+FG+ Q + G + ++G+ V+ NP DAI+ G+ L PE+RK G+V ++V++NI Sbjct: 315 TELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENI 374 Query: 368 VLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427 L +L+ G L ++ E++E YVK L IKT ++ + LSGGNQQK +LA+W+A Sbjct: 375 AL-ALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMA 433 Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVM 484 +LI DEPTRGIDV AK EI I LA G AV+ ISSE+ E++ ++ RIVV+ Sbjct: 434 IEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVL 490 Score = 113 bits (283), Expect = 1e-29 Identities = 65/212 (30%), Positives = 124/212 (58%), Gaps = 6/212 (2%) Query: 33 VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92 +D ++ E+V L G G+G++ L ++L G+ +PD G + ++G+ V+F +P+DA + G++ Sbjct: 294 LDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLA 353 Query: 93 VIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149 + +E + ++V ENI LA +A G + LS R ++ + R +LL + + Sbjct: 354 LCPEERKTDGIVAELSVRENIALALQARMGVGKFLS-RSEQTELAERYVKLLGI--KTET 410 Query: 150 PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISV 209 D + L+ +Q + + + EPR++ +DEPT + V + + + I L G++V Sbjct: 411 VDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAV 470 Query: 210 VFVSHRLDEVMRISDRIVVMRDGKRIGELKKG 241 +F+S + EV+R++ RIVV+RD +++GEL G Sbjct: 471 LFISSEMSEVVRVAHRIVVLRDRRKVGELPAG 502 Score = 70.5 bits (171), Expect = 1e-16 Identities = 49/210 (23%), Positives = 104/210 (49%), Gaps = 9/210 (4%) Query: 284 VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKM 343 +++V + GE+ G GAG++ + ++ GV + G + + G+ V +P A ++ Sbjct: 34 LRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRL 93 Query: 344 GIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKIS-RWGLVLDERKEEEISEDYVKRLSIKT 402 GI + ++ L ++V +NI + G +D + + D V R+ ++ Sbjct: 94 GISTVYQE---VNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQRARDLVARIGLQI 150 Query: 403 PSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGK 462 + ++ + QQ V +A+ L+ + +LI DEPT +D ++ ++R L ++G Sbjct: 151 -DVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSEGL 209 Query: 463 AVIMISSELPEILNLSDRIVVM----WEGE 488 +++ ++ L ++ +SDRI V+ W GE Sbjct: 210 SIVFVTHFLNQVYAVSDRITVLRNGSWVGE 239 Lambda K H 0.319 0.138 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: 593 Number of extensions: 25 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 520 Length of database: 517 Length adjustment: 35 Effective length of query: 485 Effective length of database: 482 Effective search space: 233770 Effective search space used: 233770 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 (21.7 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