Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_110805878.1 C8J30_RS10880 ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >NCBI__GCF_003217355.1:WP_110805878.1 Length = 352 Score = 176 bits (446), Expect = 8e-49 Identities = 102/307 (33%), Positives = 166/307 (54%), Gaps = 17/307 (5%) Query: 39 AIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIA-CAGVTTAVVIN 97 A PNF + N + +++ +A GM F + +G DLSV S + CA V+ +++ Sbjct: 36 AFMAPNFLSVANSVIVAKHAALTAFLAIGMTFVIITGGIDLSVGSTVGLCAMVSGWLILY 95 Query: 98 LTESLWIGVAAG---------LLLGVLCGLVNGFVIAKLKINALITTLATMQIVRGLAYI 148 + +G + +GV G VNG +I KL + I TL T+ I RG A + Sbjct: 96 GIDLGAMGTMQFNTLEIALLVMCVGVFVGFVNGILITKLNVAPFIATLGTLYIARGAALL 155 Query: 149 ISDGKAV----GIED---ESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTL 201 S G+ G D SF +G + GLP IW+ +A ++ + +T GR+ Sbjct: 156 SSGGRTFPNLSGNADYGSASFPGIGAGTFLGLPVQIWMLIAVGLVAAYIAKRTPLGRHIY 215 Query: 202 AIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISA 261 A+GGNE A L+GV V R K+ +++ SG +AI G+I+AS++ + P T +EL I+A Sbjct: 216 AVGGNERGAALSGVKVNRVKLFVYMFSGFCAAIVGLIIASQLQAAHPATGETFELNAIAA 275 Query: 262 CVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYK 321 VLGG SL GG GKI + G ++ + + + ++++S F Q V++GL+++AAV+ D+ + Sbjct: 276 AVLGGTSLSGGRGKIGGTIVGAFVISILSDGLVMMSVSSFWQTVIKGLVIVAAVVIDQAQ 335 Query: 322 QKAKRTV 328 K + V Sbjct: 336 SKLQARV 342 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: 314 Number of extensions: 23 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: 352 Length adjustment: 28 Effective length of query: 300 Effective length of database: 324 Effective search space: 97200 Effective search space used: 97200 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 24 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