Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_011842435.1 RSPH17029_RS17920 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_000015985.1:WP_011842435.1 Length = 430 Score = 306 bits (784), Expect = 8e-88 Identities = 164/425 (38%), Positives = 261/425 (61%), Gaps = 8/425 (1%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFVLA 64 IL +F++ +++G+PVA ++GL+A+ G IPL ++ S VN F ++A+P FVLA Sbjct: 6 ILTLAFVLFLILGVPVAVSIGLAAVAGMIVAGIPLSYVVQAAYSAVNDFLIIAVPMFVLA 65 Query: 65 GAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPE 124 G +M +GG+++RL+AF+ LVG GGL+ V I+A TFF AISGS A A++GS++IP Sbjct: 66 GVLMEKGGLTQRLIAFSRTLVGRSPGGLASVTIVACTFFAAISGSGPATAAAIGSIMIPT 125 Query: 125 MERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSA 184 M ++GY + F+ A+T + ++ PPS ++Y + A VSI LF+AG++PGL+L+ Sbjct: 126 MIKEGYHKSFAAAITSNAGGIGVVIPPSIPMIIYGITA--EVSITGLFIAGVIPGLMLAV 183 Query: 185 VMMGLCLIFAKKRNY----PKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE 240 + + + KR Y P+G L+ A EA W L+A +IILGGI +G+FT TE Sbjct: 184 ALTAVSRYISTKRGYAVANPEGR--SLKRIGAAAWEARWALLAPIIILGGIYTGIFTVTE 241 Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS 300 ++ VAV+++ FV +FIYR M VR +V+ ++ G V+T+ Q+P Sbjct: 242 ASIVAVLYALFVGIFIYRTITLPGFIDSMSYAVRLTGVVLFVLVSGRLLGRVLTIFQVPQ 301 Query: 301 KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM 360 + + + DN V+++ I +L+ +G M+ ++ILTP+LLPV G+DP+ FG+ Sbjct: 302 EFSAFMIATFDNPVVLVLLIIALLIFVGMWMETLTQLIILTPLLLPVAVSAGIDPIQFGI 361 Query: 361 IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420 + ++ IG TPP+G LFV S I ++E KA +P A +VL+ VT+IP +SL+ Sbjct: 362 MFVIACEIGYSTPPLGVNLFVASEISNETVERVSKAALPLIAAEIVVLLLVTFIPQLSLF 421 Query: 421 LPSVV 425 LP ++ Sbjct: 422 LPRLM 426 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: 537 Number of extensions: 30 Number of successful extensions: 3 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: 430 Length adjustment: 32 Effective length of query: 394 Effective length of database: 398 Effective search space: 156812 Effective search space used: 156812 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 Apr 10 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