Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 3609946 Dshi_3328 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Dino:3609946 Length = 426 Score = 301 bits (772), Expect = 2e-86 Identities = 166/423 (39%), Positives = 263/423 (62%), Gaps = 5/423 (1%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWID--IPLQAMMIQVASGVNKFSLLAI 58 M F + + + +I + +P+A AL +SA++G ++ L + + + +G KFSL+AI Sbjct: 1 MLMFGIFVAMVAMICLNIPIAVALAVSAILGLLVMEGTSSLVTVALDMYNGSTKFSLIAI 60 Query: 59 PFFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVG 118 P FVLAGAIM GG++ RL+ F ++GFVRGGL+ VNI S FF ISGS+VAD A++G Sbjct: 61 PMFVLAGAIMNAGGITDRLINFVTCIIGFVRGGLAHVNIGVSLFFAEISGSAVADVAAMG 120 Query: 119 SVLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMP 178 SV+IP+M+++GY FS AVT S + A++ PPS +LY+ +A VS+ LF+AGI+P Sbjct: 121 SVMIPQMKKRGYSGAFSAAVTSSSASLAIIIPPSIPMILYATSA--NVSVEQLFVAGIVP 178 Query: 179 GLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTA 238 GL+ +A +MG+ +FA++ + P+ E R + +AL VIILGGI G TA Sbjct: 179 GLMGAAGLMGVAYVFARRYDLPREEAFSGRRLWETFIDALPTFALPVIILGGIFGGFVTA 238 Query: 239 TESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQI 298 TE+A +AV+ + V+++ YR L M ++VM+L+ + G +T Q+ Sbjct: 239 TEAAGLAVLAAILVSLY-YRQVNLGRLKSAMLDGGMQTAVVMVLVAASVVMGGFLTRAQV 297 Query: 299 PSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHF 358 P +I L ++DN++VIL+ +NF +++G + A I+++ PI++P+I ++P+HF Sbjct: 298 PQEIAQNILEITDNKWVILLILNFFFLIIGFFLHSAAAIILVVPIVIPLIVAADINPIHF 357 Query: 359 GMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAIS 418 G+++ +NL IG TPPV +VL A+ + +I K + F L L VL+ TYIP+I Sbjct: 358 GLVVTLNLAIGQQTPPVASVLITACAVARANIWEVSKVNIWFILVLLTVLLMCTYIPSIP 417 Query: 419 LWL 421 L+L Sbjct: 418 LFL 420 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: 555 Number of extensions: 23 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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