Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >lcl|FitnessBrowser__Miya:8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq) Length = 640 Score = 344 bits (882), Expect = 5e-99 Identities = 180/423 (42%), Positives = 270/423 (63%), Gaps = 10/423 (2%) Query: 4 FILLGSFIVLILIGMPVAYALGLSAL---IGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 ++L G F++ +L+G+P+A++LGL+ + +GA + + A + V+ ++ F +LAIPF Sbjct: 222 WLLFGYFVLFLLVGVPIAFSLGLATIATVLGAGTLPLEYLAQIAFVS--IDSFPILAIPF 279 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 F+ AG M GG+SRRL+A LVG + GG++L I+ FF AISGS A A++GS+ Sbjct: 280 FIAAGVFMGAGGLSRRLLALGDELVGALPGGMALATIVTCMFFAAISGSGPATVAAIGSI 339 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180 IP M +GY + F+ AV S ++ PPS+ V+Y +AA S+ LF+AGI+PG+ Sbjct: 340 TIPAMVERGYDKFFAAAVVASAGCIGVMIPPSNPFVVYGVAA--QASVGKLFLAGIVPGV 397 Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVI--PLREALKIAGEALWGLMAMVIILGGILSGVFTA 238 L +M + + K+ + +GE R ++ EA W L+ VI+LGGI G+ T Sbjct: 398 LCGLALMAVAYYISLKKGW-RGEARHRDFRSVMQAMWEAKWALLVPVIVLGGIYGGIMTP 456 Query: 239 TESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQI 298 TE+AAV+ ++ V +FIYR+ WR + M + +T S++++L+ A FG +MT+ Q+ Sbjct: 457 TEAAAVSALYGMIVGLFIYREITWRRMWDCMVESAQTSSVIIVLMAMATLFGNIMTIEQV 516 Query: 299 PSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHF 358 P I L ++ N+ IL+ IN L+ +GT M+ I+I+TPILLP++T +GVDP+HF Sbjct: 517 PDHIAAMILGVTSNKIAILLLINVFLLWVGTFMEALAAIVIITPILLPLVTQVGVDPIHF 576 Query: 359 GMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAIS 418 G+IM+VNL IG ITPPVG LFV S+I KVSI V+A PF L + +LMA+TYIPAIS Sbjct: 577 GVIMVVNLAIGFITPPVGVNLFVASSISKVSIGDVVRAAWPFLLVMIALLMAITYIPAIS 636 Query: 419 LWL 421 L L Sbjct: 637 LCL 639 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: 803 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: 640 Length adjustment: 35 Effective length of query: 391 Effective length of database: 605 Effective search space: 236555 Effective search space used: 236555 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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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