Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 336 bits (862), Expect = 1e-96 Identities = 190/487 (39%), Positives = 297/487 (60%), Gaps = 11/487 (2%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 + P L GI K F G+ L D+ + Y G++HALMG+NGAGKSTL+K+L+G + G Sbjct: 15 AAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQ 74 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPH----KGGIVNRSL 119 + + GQ + AA G++ +YQE++L P ++VAENI+ G+ P +G ++ + Sbjct: 75 MRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWAT 134 Query: 120 LNYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREI 179 L+ A + +G+ ID L + Q+V IA+AL+ ++++ DEPTSSL E+ Sbjct: 135 LHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEV 194 Query: 180 DNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239 LF V+R LR EG I++V+H + +++A+SD ITV ++G +V + + + AL+ A Sbjct: 195 QKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWL-AKDLGPQALIAA 253 Query: 240 MVGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRT-----PISLAVRSGEIVGLFGLVGAG 294 M+GRD+ + + + ++A G+ P+ L +R+GE+VGL GL+G+G Sbjct: 254 MLGRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSG 313 Query: 295 RSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354 R+EL + +FG Q G + ID Q + P AI G+ LCPE+RK +GI+ SVR+N Sbjct: 314 RTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVREN 373 Query: 355 INISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWL 414 I ++ + + +G ++ + A+ +++ L IKT ++ I LSGGNQQKAIL RW+ Sbjct: 374 IALALQARMGVGK-FLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWM 432 Query: 415 SEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMRE 474 + E ++++LDEPTRGIDV AK EI + I LA G+AVLF SS++ EV+ VA RIVV+R+ Sbjct: 433 AIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRD 492 Query: 475 GEIAGEL 481 GEL Sbjct: 493 RRKVGEL 499 Score = 78.2 bits (191), Expect = 7e-19 Identities = 65/227 (28%), Positives = 109/227 (48%), Gaps = 14/227 (6%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334 + L + GEI L G GAG+S L+K + G + + GQ+ + Q + P +AA + Sbjct: 37 VQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAV---WPDSPLAAQRL 93 Query: 335 LCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTP--- 391 + + P SV +NI + C I G+ + A H R+ ++ Sbjct: 94 GISTVYQEVNLCPNLSVAENIFAGRYPR-----CGIAQGFRIDWATLHQRARDLVARIGL 148 Query: 392 --GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQG 449 +L+ + QQ + R LS E +V++LDEPT +D +++ V+ L ++G Sbjct: 149 QIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSEG 208 Query: 450 VAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAM 496 ++++F + L +V V+DRI V+R G GE L + QAL AM Sbjct: 209 LSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGP-QALIAAM 254 Lambda K H 0.319 0.136 0.391 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: 604 Number of extensions: 33 Number of successful extensions: 8 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: 504 Length of database: 517 Length adjustment: 35 Effective length of query: 469 Effective length of database: 482 Effective search space: 226058 Effective search space used: 226058 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