Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 251 bits (642), Expect = 3e-71 Identities = 169/509 (33%), Positives = 259/509 (50%), Gaps = 32/509 (6%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 +TP L+ I K +PGV A D+S G++HA++GENGAGKSTL+KI+ G P G Sbjct: 5 TTPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGD 64 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG---------QLPHKGGI 114 + NG + + A N G+A+++Q L +TVAENI LG PH G Sbjct: 65 MHFNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAG-- 122 Query: 115 VNRSLLNYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSL 174 N L + G+ ++P+ + LS+G+ Q VEI +AL +++ DEPTS L Sbjct: 123 TNMKQLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVL 182 Query: 175 SAREIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHD 234 + + + LF +R+L EG ILY+SH+++EI L + TV + GR V D +Q Sbjct: 183 TPQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGR-VTGVCDPRQESAA 241 Query: 235 ALVQAMVGRDIGDIYGWQPRSY------GEERLRLDAVKAPGVR------TPISLAVRSG 282 +L + M+G G PR G RL + + P ISL +R+G Sbjct: 242 SLSRLMIG-------GEPPREARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAG 294 Query: 283 EIVGLFGLVGAGRSELMKGMFG-GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRK 341 EIVG+ G+ G G+ EL+ + G + + +D +P+ AG+ PE+R Sbjct: 295 EIVGIAGVSGNGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERL 354 Query: 342 AEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLS 401 G +P S+ NI +S + + +I+ A I L +K G L +LS Sbjct: 355 GRGAVPGMSLAANILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLS 414 Query: 402 GGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPE 461 GGN QK I+GR + KV+++ +PT G+DVGA +I+N + AL A G A+L S +L E Sbjct: 415 GGNLQKFIVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDE 474 Query: 462 VLGVADRIVVMREGEIAGELLHEQADERQ 490 + + DR+ V+ +G ++ + A Q Sbjct: 475 LFAICDRLHVIAKGRLSPSIPTRDATREQ 503 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: 646 Number of extensions: 40 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: 529 Length adjustment: 35 Effective length of query: 469 Effective length of database: 494 Effective search space: 231686 Effective search space used: 231686 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