Align Tricarboxylate transport membrane protein TctA (characterized)
to candidate WP_086509569.1 BZY95_RS08765 tripartite tricarboxylate transporter permease
Query= reanno::Dino:3609738 (505 letters) >NCBI__GCF_002151265.1:WP_086509569.1 Length = 496 Score = 488 bits (1256), Expect = e-142 Identities = 255/497 (51%), Positives = 349/497 (70%), Gaps = 16/497 (3%) Query: 5 LLIGLQTAFSIQNLAMVIGGCLIGTFIGMLPGLGPMSIIAIMIPVAISLGDPSAALILLA 64 L+ G A N+ V G GT IGMLPGLGP+S +A+MIP+ + +PS+ LIL+A Sbjct: 7 LMYGFSIALEPINILYVFAGVFAGTIIGMLPGLGPISALALMIPLTFGM-EPSSGLILMA 65 Query: 65 GVYYGAIFGGSTSSILLNAPGVAGTVATSFDGYPMAQQGKAGKALTIAAIASFAGGTIGA 124 GVYYGAIFGGSTSSILLNAPGVAGTVATSFDGYPMA+QG AGKAL IAA ASF GGT+ Sbjct: 66 GVYYGAIFGGSTSSILLNAPGVAGTVATSFDGYPMAKQGMAGKALAIAAYASFIGGTVSI 125 Query: 125 ILLMVFAPALSSVALLFHSAEYFALMVVGLSAIAAFAGTGQVAKALLMTILGLIMATVGE 184 I LM+ AP L VA+ F AEYF+LMV+GL+A+ + + V K L+ ++G++++ +G Sbjct: 126 IFLMMVAPLLGRVAVSFGPAEYFSLMVLGLTAVVSLSDKSLV-KGLIAAVVGVMISIMGI 184 Query: 185 GALFASPRFTMGLMDLQSGFGFITLAMAMFALPEALFLVMNPLRAASGQGGGE-----IK 239 + RFT G + L G F+ +A+ +FAL E ++++ G GG E I Sbjct: 185 DLQTGTERFTFGTVHLLDGIEFLVVALGIFALAEVFYMLLK------GGGGKEQPRNAIG 238 Query: 240 DLRITRAEARSIAPVIGRQSVQGFFIGVLPGAGATIASFLGYAVERNIASKDEQAEFGKG 299 L++++ E + IAP IGR S+ GFF GVLPGAGATI SFLGY++E+ +A + FGKG Sbjct: 239 SLKLSKQEIKQIAPPIGRSSILGFFTGVLPGAGATIGSFLGYSMEKRLAKDGDT--FGKG 296 Query: 300 SVKGLAAPETANNAACTGSFVPLLTLGIPGSGTTAILLGALLALNVSPGPRLMIDAPEIF 359 ++KG+AAPE+ANNAACTGSFVPLLTLG+PGSG+TA+LLGALL + VSPGP +++D P++F Sbjct: 297 NIKGVAAPESANNAACTGSFVPLLTLGVPGSGSTAVLLGALLVMGVSPGPAMLVDRPDVF 356 Query: 360 WAVIMSMFIGNLVLLILNLPLIPYIAKILSVPRNYLIPFILFFTLMGAYIGQNNATELLL 419 W V+ SM++GN+ LL+LNLPLIP IAKIL +PR L+ IL F ++G Y + +LLL Sbjct: 357 WGVVASMYLGNIFLLVLNLPLIPLIAKILDLPRPLLLSLILIFCMIGVYGMSFSVFDLLL 416 Query: 420 LVGFGICATILKFADYPLAPLLIGFILGGLLENNFSRAMQLYDG-ISFIWERPMTLGLLV 478 L+GFG+ ++ +P APL++ ILG ++E + RA+Q+ G S ++P+++ LL+ Sbjct: 417 LLGFGLLGLGMRLFGFPAAPLILALILGDIMEESMRRALQISGGDWSIFIDKPISMWLLI 476 Query: 479 IAALLIILPSYRNRRAK 495 IAAL + LP + A+ Sbjct: 477 IAALSLTLPLIKRVMAR 493 Lambda K H 0.326 0.143 0.411 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: 838 Number of extensions: 52 Number of successful extensions: 6 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: 505 Length of database: 496 Length adjustment: 34 Effective length of query: 471 Effective length of database: 462 Effective search space: 217602 Effective search space used: 217602 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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