Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 374 bits (961), Expect = e-108 Identities = 211/506 (41%), Positives = 327/506 (64%), Gaps = 22/506 (4%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDA--GEI 71 +L+ + I K FPGVVA++ V+ +V EI +++GENGAGKSTL+K+L+GV + G+I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 72 LVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDEN 131 L +G+ EF D+ GI +IHQEL L +++AENIFL E R +D Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETAR------HGVIDWM 115 Query: 132 YMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEE 191 ++R++ LL +G SPD V L ++Q+VEI KAL ++ R++ +DEPT+SL + Sbjct: 116 AAHSRAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNEND 175 Query: 192 TERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGEL--KKGEFDVDTII 249 ++ L +++ LK++GI+ + +SH+L+E+ R++D I V+RDG + L ++G D +I Sbjct: 176 SQALLDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVI 235 Query: 250 KMMVGREVEFFPHGIETRPGEIALEVRNLKW-------KDKVKNVSFEVRKGEVLGFAGL 302 + MVGRE+ + + GEI EVRN + ++ +K + VR+GE++G AGL Sbjct: 236 QAMVGREMSDRYPQRQPQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGL 295 Query: 303 VGAGRTETMLLVFGVN--QKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLR 360 +GAGRTE + +FG + Q+ SG++ ++G+ +++ E A+ G+ + EDRK GLVL Sbjct: 296 MGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLN 355 Query: 361 MTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKV 420 ++ N L +L +S + V+D +E +++DY ++L I+ + Q T NLSGGNQQKV Sbjct: 356 EDIQFNTSLANLPGVS-FASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKV 414 Query: 421 VLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDR 480 VL+KWL T+ ++LI DEPTRGIDVGAK EI+ +I +LAA+GK VI+ISSE+PE+L ++DR Sbjct: 415 VLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDR 474 Query: 481 IVVMWEGEITAVLDNREKRVTQEEIM 506 I VM EG A + E +QE+IM Sbjct: 475 IYVMNEGRFVAEMPTSE--ASQEKIM 498 Score = 82.4 bits (202), Expect = 4e-20 Identities = 68/247 (27%), Positives = 127/247 (51%), Gaps = 13/247 (5%) Query: 273 LEVRNLKWKDK----VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGV--NQKESGDIY 326 LE+RN++ + V+ +V+ GE+ G GAG++ M ++ GV + SG I Sbjct: 3 LEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQIL 62 Query: 327 VNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERK 386 +G++ E D+ +GI +I ++ L L +++ +NI L + + +R G V+D Sbjct: 63 FDGQEREFAGIRDSEHLGIIIIHQELALVPL---LSIAENIFLGN--ETARHG-VIDWMA 116 Query: 387 EEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGA 446 ++ + ++ + + + L G QQ V +AK L+ +LI DEPT ++ Sbjct: 117 AHSRAQALLHKVGLGESPDTPVGQ-LGVGKQQLVEIAKALSRKVRLLILDEPTASLNEND 175 Query: 447 KAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNREKRVTQEEIM 506 + ++ EL AQG I+IS +L EI ++D I V+ +G +LD RE V+++ ++ Sbjct: 176 SQALLDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVI 235 Query: 507 YYASGQK 513 G++ Sbjct: 236 QAMVGRE 242 Score = 75.5 bits (184), Expect = 4e-18 Identities = 51/224 (22%), Positives = 109/224 (48%), Gaps = 4/224 (1%) Query: 33 VDFEVYENEIVSLIGENGAGKSTLIKILTGVL--KPDAGEILVNGERVEFHSPVDAFKKG 90 +D V EIV + G GAG++ L + G + +GE+ ++G+ ++ + A G Sbjct: 280 IDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHG 339 Query: 91 ISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFSP 150 ++ + ++ + + + E+I + +S +D + +++ + + + S Sbjct: 340 LAYVTEDRK-GNGLVLNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSG 398 Query: 151 -DALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISV 209 D NL+ +Q V + K L P ++ +DEPT + V ++ +I L + G V Sbjct: 399 VDQKTLNLSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCV 458 Query: 210 VFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 + +S + E++ I+DRI VM +G+ + E+ E + I++ +V Sbjct: 459 IVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIV 502 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: 678 Number of extensions: 38 Number of successful extensions: 11 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: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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