Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 362 bits (930), Expect = e-104 Identities = 203/502 (40%), Positives = 312/502 (62%), Gaps = 12/502 (2%) Query: 6 PYL-SFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTT--G 62 PYL + I KTF VKA+ ++ AG++ +L GENG+GKSTL+K+L G Y + G Sbjct: 2 PYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEG 61 Query: 63 SVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNY 122 ++ G+E+ S G+AII+QEL LV E+TV ENI+LG GI++ L+ Sbjct: 62 EIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTL 121 Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 L + + I PDT + L +GQ Q+VEIAKAL + +++ DEPT+SL+ +E L Sbjct: 122 RCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSIL 181 Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242 +IR+L++ G +Y+SH++ E+ A+SD I V +DG+++ T D + D ++ MVG Sbjct: 182 LDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGT-RDAAGMSEDDIITMMVG 240 Query: 243 RDIGDIYGWQPRSYGEERLRLDAVKA--PGVR-----TPISLAVRSGEIVGLFGLVGAGR 295 R++ +Y +P + G+E LR++ + A P R +S +++ GEI+G+ GLVGAGR Sbjct: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300 Query: 296 SELMKGMFG-GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354 +E ++ +FG G++YID + +DIR AIA G+ + PEDRK +GI+PV +V N Sbjct: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360 Query: 355 INISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWL 414 I ++A K G +++ E+ I+ L +KT + I LSGGNQQKAIL R L Sbjct: 361 ITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCL 420 Query: 415 SEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMRE 474 ++++LDEPTRGID+GAK+EIY +I L QG+AV+ SS+LPEVLG++DR++VM E Sbjct: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480 Query: 475 GEIAGELLHEQADERQALSLAM 496 G++ L++ + Q + A+ Sbjct: 481 GKLKANLINHNLTQEQVMEAAL 502 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: 676 Number of extensions: 32 Number of successful extensions: 11 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: 504 Length of database: 513 Length adjustment: 34 Effective length of query: 470 Effective length of database: 479 Effective search space: 225130 Effective search space used: 225130 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