Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= uniprot:Q88GX3 (239 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 85.9 bits (211), Expect = 2e-21 Identities = 55/172 (31%), Positives = 92/172 (53%), Gaps = 9/172 (5%) Query: 19 LLAGALVTVSLALACLPIGLPLGLVVALAARSRKRLPRAWATTFSTVFRGLPELLTLLII 78 L G T+ L++ +G LG+V+A+A SR R R A ++ +FRGLP ++ +L++ Sbjct: 359 LKTGLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVILVV 418 Query: 79 YYGCQIAAQKILAAMGYQGEFLINTFLAAMIAFSLVFAAFSSEIWLAAFKTLPKGQLEAC 138 G + + N + +A +L+ AA+ EI+ + +++ GQLEA Sbjct: 419 GLGIGPVVKNLTGN---------NPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEAS 469 Query: 139 SALGLSKRTGFFKVLLPQLTRIALPGLSNNWLSLLKDTSLVSTISLVDLMRQ 190 A+G S R V++PQ R LP L N ++SL+KD+SLV + L+ R+ Sbjct: 470 RAIGFSYRQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRE 521 Lambda K H 0.328 0.139 0.410 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: 263 Number of extensions: 16 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: 239 Length of database: 589 Length adjustment: 30 Effective length of query: 209 Effective length of database: 559 Effective search space: 116831 Effective search space used: 116831 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 (21.8 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