Align ABC transporter permease (characterized, see rationale)
to candidate YP_428497.1 Rru_A3416 inner-membrane translocator
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000013085.1:YP_428497.1 Length = 290 Score = 120 bits (300), Expect = 5e-32 Identities = 89/301 (29%), Positives = 144/301 (47%), Gaps = 22/301 (7%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 LL NG V+G + AL AL T+V+GI + N A G+V GA + GA+P Sbjct: 6 LLNLAFNGAVIGLITALAALSITLVFGIARFPNAATGDVATAGAFAGLLGPVLGSGALP- 64 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 ++ +A ++ + V +R L +A LI +IGM+ L+ + Sbjct: 65 ---------IILVGMATSAAVSLLFYVVLFRALAKRSPVASLIASIGMAFFLRAVLTYFI 115 Query: 124 KPNYKPYPTMLPSS-PFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAE 182 + + YP L + PF G + I ++ ALA L++ T +G+ MRA A+ Sbjct: 116 GHDQRVYPLPLVRAVPF--GPLRVQAADIQVIVWAGAALAVTFALIHLTPIGKRMRAVAD 173 Query: 183 NPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFG 242 NP +A G+ + V+ +++ +LA +AG + MG+ + AF A + G Sbjct: 174 NPDLARSSGINANKVMVVMWVVAGLLAGLAGTLLGVK-TVVSPEMGWDLLMPAFAATILG 232 Query: 243 GIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLG 302 IGN GAV+GG+L+GL + L+ L+G Y F+VL++ L +RP GL Sbjct: 233 TIGNPLGAVLGGLLIGLAQ--------ELSTPLVGFTYKIGVGFLVLLLTLLIRPQGLFA 284 Query: 303 E 303 + Sbjct: 285 K 285 Lambda K H 0.327 0.142 0.419 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: 203 Number of extensions: 13 Number of successful extensions: 4 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: 309 Length of database: 290 Length adjustment: 27 Effective length of query: 282 Effective length of database: 263 Effective search space: 74166 Effective search space used: 74166 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 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