Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_011383335.1 AMB_RS04550 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_000009985.1:WP_011383335.1 Length = 427 Score = 313 bits (802), Expect = 6e-90 Identities = 152/423 (35%), Positives = 263/423 (62%), Gaps = 3/423 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAW-WIDIPLQAMMIQVASGVNKFSLLAIP 59 M + ++ G IVL+L GMP++ +LGL+ L + + +P++++ +++ +G+ KF ++AIP Sbjct: 1 MNSAVIFGLLIVLMLTGMPISISLGLTVLSFLFLFTQVPIESVALKLFTGIEKFEIMAIP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG + GG++RR++ FA +VG GGL L +MA F A+SGSS A ++GS Sbjct: 61 FFILAGNFLTHGGVARRMINFATAMVGHWYGGLGLAGVMACALFAAVSGSSPATVVAIGS 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +++P M ++G+P +F V + +L PPS V+Y++A S+ +LFMAG++PG Sbjct: 121 IILPAMVKQGFPNKFGAGVITTSGALGILIPPSLVMVMYAVAT--NTSVGALFMAGVIPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 L+L+ V+ + A K +YP+ + + EA+WGL +VI++GGI +GVFT T Sbjct: 179 LVLATVLGAVTWYIAWKNDYPRLPPATWAQRFRAFREAIWGLALIVIVIGGIYTGVFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+AA++ V++F + +F+Y+D + + K++ + ++++ +I A F +V+ IP Sbjct: 239 EAAAMSAVYAFLIAVFVYKDMPLKGVGKILLSSASMSAMLLYIITNAVLFSFVLANENIP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 I + L+ +N +L++ G M+ + ++LI+ PIL PV +G+DP+HFG Sbjct: 299 HAIADWIVGKELGVIAFLLVVNVLLLVAGNFMEPSSIVLIMAPILFPVAMKLGIDPIHFG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 ++++VN+ +G+ PPVG L+V S I K+ I A+ P+ LA+ LM VTY P +S+ Sbjct: 359 ILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLAMLGFLMVVTYWPPLSI 418 Query: 420 WLP 422 WLP Sbjct: 419 WLP 421 Lambda K H 0.329 0.142 0.418 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: 586 Number of extensions: 40 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: 426 Length of database: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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