Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 173 bits (439), Expect = 5e-48 Identities = 98/308 (31%), Positives = 165/308 (53%), Gaps = 4/308 (1%) Query: 23 DQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82 ++ G+LVV A+L++ ++ P F + N + + G+ A M + SG+ D+SV Sbjct: 25 NEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVG 84 Query: 83 SVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142 ++A V A ++ L + LLLG L G + G + + + + TL + Sbjct: 85 PMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLWSAL 144 Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202 RG+ +++ V I++ + G+P + + +F + KT FGR+ A Sbjct: 145 RGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKTAFGRSVFA 204 Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262 +GGN AA+L G+ V R +I+IF LSGL++A+ GI+LA+R+ SG + G E VI+A Sbjct: 205 VGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEFDVIAAV 264 Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLIL----LAAVIFD 318 V+GG +L GG G + + G+L++ + N + LL I+ F Q VVRG+I+ LA ++ Sbjct: 265 VVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVAVLANILLT 324 Query: 319 RYKQKAKR 326 + KAKR Sbjct: 325 QRSSKAKR 332 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: 338 Number of extensions: 24 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: 332 Length adjustment: 28 Effective length of query: 300 Effective length of database: 304 Effective search space: 91200 Effective search space used: 91200 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: 49 (23.5 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