Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 313 bits (802), Expect = 6e-90 Identities = 163/427 (38%), Positives = 264/427 (61%), Gaps = 8/427 (1%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSA----LIGAWWIDIPLQAMMI--QVASGVNKFS 54 M IL G ++L + PVA ALG +A L + + L+ M+ ++ +G + F Sbjct: 1 MVGLILFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFP 60 Query: 55 LLAIPFFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADT 114 LLA+P F+LAG +M+ GG+SRR+VA A LVG + GGL+ V+++++ FF +SGS+ ADT Sbjct: 61 LLAVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADT 120 Query: 115 ASVGSVLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMA 174 A+VGS+LIP M R+GYP + AV +G ++ PPS +++ G SI LF Sbjct: 121 AAVGSILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGA--SIGRLFAG 178 Query: 175 GIMPGLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSG 234 G++PGLL+ A ++ LC++ A++ R W L A IILG I+ G Sbjct: 179 GVLPGLLMGASLVALCVVEARRTGRVPERRFDARALWPAIRSGAWALGAPAIILGTIIGG 238 Query: 235 VFTATESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMT 294 V TATESAA+AV ++ V ++ +R+ +WRDLP+L T ++VM++I A+ FG+VM Sbjct: 239 VATATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWVMA 298 Query: 295 LMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVD 354 L ++P I L+LS +R V+L+ +N +L+++G ++ IL+ P+L+P++ +G+D Sbjct: 299 LERLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALGID 358 Query: 355 PVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYI 414 VH G+I++VNL IG++TPP+G L V +I ++ + + +A++P + L + L+ VT+ Sbjct: 359 LVHLGVIVVVNLAIGMLTPPLGVCLVVSCSIARIPLSAISRAIVPMLVVLIVDLLLVTFF 418 Query: 415 PAISLWL 421 P + LWL Sbjct: 419 PPLVLWL 425 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: 598 Number of extensions: 36 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: 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