Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__BFirm:BPHYT_RS01810 Length = 319 Score = 196 bits (498), Expect = 6e-55 Identities = 117/311 (37%), Positives = 176/311 (56%), Gaps = 11/311 (3%) Query: 27 MLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIA 86 +L+ A L + + +F + N+ SM +++ GM F + +G DLSV +V A Sbjct: 7 ILLALAALVVFGLVRYEHFGSAYNITSFWRYNSMFALISVGMAFVIITGGIDLSVGTVAA 66 Query: 87 CAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVRGLA 146 A V A + W+ V AG G+ G++NG +I +LKI I TLAT G+A Sbjct: 67 LASVVAA--LTSVYGGWVAVLAGCGAGLAVGVLNGLIITRLKILPFIVTLATSLGAHGVA 124 Query: 147 YIISDGKAVGIEDESFFA-LGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAIGG 205 ++ AV I ES F G + FGLP P + V + L L T FGR++LAIGG Sbjct: 125 LLLGKNDAVSIAAESNFGNFGQGDLFGLPIPGIVAVVAAVAGWLALRSTRFGRHSLAIGG 184 Query: 206 NEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACVLG 265 +EEAARL G+ V RT ++ + +SGL++ +AG+ILA++ +GQP +G+EL ISA VLG Sbjct: 185 SEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQPNEGVGWELFAISAVVLG 244 Query: 266 GVSLKGGIGKISYVVAGILILGTV------ENAMNLLNISPFAQYVVRGLILLAAVIFDR 319 G L GG G I+ +AG+L+LG V EN + +++S + Q V+RG+ LL ++ Sbjct: 245 GTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYWQSVIRGVFLLLVIVLQA 304 Query: 320 --YKQKAKRTV 328 KQ+ ++ V Sbjct: 305 RVLKQRGRKRV 315 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: 378 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 319 Length adjustment: 28 Effective length of query: 300 Effective length of database: 291 Effective search space: 87300 Effective search space used: 87300 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