Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 374 bits (959), Expect = e-108 Identities = 204/484 (42%), Positives = 309/484 (63%), Gaps = 6/484 (1%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64 P+LQ+ GI K F L D+ L + PGEIHALMG+NGAGKSTL+KVL+GV G++ Sbjct: 17 PVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMR 76 Query: 65 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL---IDHAAMR 121 L G+ V P A++ GI+ +YQE+ + PN+SVA N+F G R + ID A + Sbjct: 77 LGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLH 136 Query: 122 SRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQ 181 R ++ ++G + L +A QQ V IARAL SR++I+DEPT++L + E ++ Sbjct: 137 QRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQK 196 Query: 182 LFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241 LF V+RRLR EGL+I++++H + +VYA++DR+TVLR+GS+VGE + ++ + ++ M+G Sbjct: 197 LFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLG 256 Query: 242 RSLSEFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTE 300 R L+ + APA ++ ++Q L +++P +RAGEV+G AGL+G+GRTE Sbjct: 257 RDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRTE 316 Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360 LARLLFG + G + ++G+ V P A+R G+A PE+RK G+ +++V N + Sbjct: 317 LARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIAL 376 Query: 361 NVASRHTRLGLVRSRS-LGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419 + +R +G SRS +A ++ L +K + P+G LSGGNQQK +LARW+ I Sbjct: 377 ALQAR-MGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIE 435 Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479 P++LILDEPTRG+D+ AK EI + RLA G+AV+ ISSE+ EV+ + R++V+R+ Sbjct: 436 PRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRK 495 Query: 480 TGEL 483 GEL Sbjct: 496 VGEL 499 Lambda K H 0.320 0.135 0.378 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: 720 Number of extensions: 31 Number of successful extensions: 8 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: 521 Length of database: 517 Length adjustment: 35 Effective length of query: 486 Effective length of database: 482 Effective search space: 234252 Effective search space used: 234252 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