Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate SM_b21375 SM_b21375 sugar uptake ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Smeli:SM_b21375 Length = 320 Score = 215 bits (548), Expect = 1e-60 Identities = 118/308 (38%), Positives = 185/308 (60%), Gaps = 1/308 (0%) Query: 20 RIWDQYG-MLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFD 78 R QYG + + +L I + F P F T +N + +++ + A GM + + G+ D Sbjct: 13 RALKQYGGIFLSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTWVILLGEID 72 Query: 79 LSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLAT 138 LSV S+IA AG+ A +A L G L G++NG + AKL + + I T+AT Sbjct: 73 LSVGSIIAVAGMVGAQCFAFGMGFAPAIALTLAAGALMGMLNGVLTAKLLLPSFIVTVAT 132 Query: 139 MQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGR 198 M I RG+ + ++G IE+E++ A+G ++ GLP IW+ +I ++L+KT+FGR Sbjct: 133 MGIYRGMVSLPTNGAPAMIENETWTAIGTESFLGLPIIIWVVAVLFVINQIVLSKTSFGR 192 Query: 199 NTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIV 258 GGN EAA +G+ V R KI+IF++SG+++AI+G++L+SR+ S Q + YEL Sbjct: 193 RAYLTGGNREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQTNAGMSYELDA 252 Query: 259 ISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFD 318 I+A VLGG SL GG+G + + G LI+G + N MN+L++ F Q +V+GL++L AV D Sbjct: 253 IAAAVLGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKGLVILVAVWLD 312 Query: 319 RYKQKAKR 326 ++AKR Sbjct: 313 VRAKQAKR 320 Lambda K H 0.327 0.141 0.414 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: 329 Number of extensions: 15 Number of successful extensions: 2 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: 328 Length of database: 320 Length adjustment: 28 Effective length of query: 300 Effective length of database: 292 Effective search space: 87600 Effective search space used: 87600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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