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) >FitnessBrowser__Miya:8501197 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:
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