Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 377 bits (967), Expect = e-109 Identities = 207/506 (40%), Positives = 327/506 (64%), Gaps = 23/506 (4%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L+ + I K F GVKAL D+S + AG+V A++GENGAGKSTL+KILSG Y G++ N Sbjct: 2 LTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYN 61 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKG-GIVNRSLLNYEAGL 126 G + F +T A G+ II+QEL+L+P +++ ENI+LG+ P G+++ + ++ EA Sbjct: 62 GDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAAQ 121 Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186 L L +++DP+TP+ L +GQ Q+VEIAKAL+ +++I DEPTS++S +E++ LF +I Sbjct: 122 LLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGII 181 Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246 R LR EG+ I Y+SH+++E+FA++D V +DG+ +++ +M+ + +AL+Q MVGR+I Sbjct: 182 RALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIES-GEMEGMTEEALIQKMVGREIV 240 Query: 247 DIYGWQPRSYGEERLRLD--AVKAPGVRTP-----ISLAVRSGEIVGLFGLVGAGRSELM 299 R + E L + VK P + I+ + GE++G+FGL+GAGR+ELM Sbjct: 241 IERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELM 300 Query: 300 KGMFG-----GTQIT-AGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRD 353 + +FG G +IT AG+V+ + +KP A+ AG+ L PEDRK +G++ + Sbjct: 301 EALFGVLPHQGAEITLAGKVH------EFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCT 354 Query: 354 NINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRW 413 N +++ +L G ++++ E+ A ++ L IK QL+ LSGGNQQK +L +W Sbjct: 355 NSSLTVVDS-ILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKW 413 Query: 414 LSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMR 473 L+ KV++LDEPTRGID+ AK+EIY +I LA +G+ ++ SS+LPE+L V+DR++VM Sbjct: 414 LATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMA 473 Query: 474 EGEIAGEL-LHEQADERQALSLAMPK 498 EG + + + Q E + L A+PK Sbjct: 474 EGRLTANIPIDAQTSEDEILQAAIPK 499 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: 670 Number of extensions: 37 Number of successful extensions: 9 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: 502 Length adjustment: 34 Effective length of query: 470 Effective length of database: 468 Effective search space: 219960 Effective search space used: 219960 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