Align ABC transporter permease (characterized, see rationale)
to candidate YP_001312923.1 Smed_4185 inner-membrane translocator
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000017145.1:YP_001312923.1 Length = 537 Score = 144 bits (363), Expect = 5e-39 Identities = 94/296 (31%), Positives = 156/296 (52%), Gaps = 12/296 (4%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAP 65 Q + GL LGS+ L A+G + +G++ +IN AHGE++M+GA T++ +++ + P Sbjct: 243 QNVWYGLSLGSVLLLAAIGLAITFGVMGIINMAHGEMVMLGAYTTFLVQDVVRTSFPHLF 302 Query: 66 GWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKP 125 W L +A +A + T+ V+E+ R L P L L+ G+S++LQ I+ P Sbjct: 303 EWS-LAIALPLAFLFTGTVGLVLERGVIRFLYGRP-LETLLATWGISLILQQSVRTIFGP 360 Query: 126 -NYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENP 184 N + S FE+GG IT ++ I+ A+L++L+ T +G MRA +N Sbjct: 361 TNREVGNPFWMSGAFELGGLTITWNRLWIIVFALAVFAALLFLLKKTPMGLQMRAVTQNR 420 Query: 185 RVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGI 244 R+AS MG++ +V + TF +G+ +A IAG+ S +G + +F VFGG+ Sbjct: 421 RMASSMGIRTPLVDALTFALGSGIAGIAGVA-LSQIDNVSPNLGQGYIIDSFMVVVFGGV 479 Query: 245 GNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GNL G +VG LG++ Y G + G +L +++I+ + RP GL Sbjct: 480 GNLWGTLVGAFSLGILNKFLEPYAGAVLGKIL--------VLVLIILFIQKRPRGL 527 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: 298 Number of extensions: 11 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: 309 Length of database: 537 Length adjustment: 31 Effective length of query: 278 Effective length of database: 506 Effective search space: 140668 Effective search space used: 140668 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: 50 (23.9 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