Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_092484450.1 BM299_RS11930 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_900115975.1:WP_092484450.1 Length = 425 Score = 334 bits (857), Expect = 3e-96 Identities = 171/423 (40%), Positives = 275/423 (65%), Gaps = 3/423 (0%) Query: 3 AFILLGSFIVLILIGMPVAYALGLSALIGAWWI-DIPLQAMMIQVASGVNKFSLLAIPFF 61 + IL SF VL+LIG+PVA++LGLS++ + IPL + ++ +G + F L+AIPFF Sbjct: 2 SLILFASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDSFPLMAIPFF 61 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 ++AGA+M GG+SRRLV FA +VG GGL+ V MAS F A+SGS A TA++G ++ Sbjct: 62 MMAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGGMM 121 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 IP + +KGY +EF++A+ S ++ PPS VL+ +G VSIA LF+AGI+PG+L Sbjct: 122 IPALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSG--VSIAELFLAGIVPGVL 179 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241 ++ ++M + K E +P +E ++ AL L+ IILGGI SG FT TE+ Sbjct: 180 IAVLLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEA 239 Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301 A +AVV+ F V +F+YR+ ++ + M V + ++V++L+ FA++F ++M IP K Sbjct: 240 AVIAVVYGFIVGIFVYRELNLANIMEAMKDAVISNAVVLMLLAFASTFSWIMASELIPQK 299 Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361 I +++ N+++ L+ + L+++GT ++ P +++L PIL+PV V+ VHFG++ Sbjct: 300 IAALMSSIAPNQFIFLLLVTVFLLIIGTFLETTPALILLVPILVPVAQTFDVNLVHFGVL 359 Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421 M+VNL IG++TPP+G LFV S I KV + + +A++PF L + L+ +T++P ISL++ Sbjct: 360 MVVNLAIGMVTPPLGITLFVASNISKVPLANLFRAIVPFILCMIAALLVLTFVPQISLFV 419 Query: 422 PSV 424 P + Sbjct: 420 PEL 422 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: 581 Number of extensions: 30 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 394 Effective length of database: 393 Effective search space: 154842 Effective search space used: 154842 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 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