Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate BWI76_RS24135 BWI76_RS24135 c4-dicarboxylate permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Koxy:BWI76_RS24135 Length = 433 Score = 402 bits (1032), Expect = e-116 Identities = 204/427 (47%), Positives = 297/427 (69%), Gaps = 6/427 (1%) Query: 3 AFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQV----ASGVNKFSLLAI 58 A +L GSF +L+ IG+P+++++G+ A +G+ + P +I V A+G++ F+LLAI Sbjct: 6 ALMLFGSFFILVFIGVPISFSIGI-ATVGSMLLMFPWDIAVITVSQRLANGLDNFALLAI 64 Query: 59 PFFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVG 118 PFF+ AG +M GG++ RL+ A V+VG V G L VN++A+ FG+ISGS+VA A+VG Sbjct: 65 PFFIFAGTLMNSGGIAIRLINLAQVMVGRVPGSLGHVNVLANMMFGSISGSAVAAAAAVG 124 Query: 119 SVLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMP 178 L P RKGY FSTAV VS + LL PPS+ +++SL AGG VS+ASLFMAG +P Sbjct: 125 GTLNPIQTRKGYDPAFSTAVNVSSCITGLLIPPSNVLIVFSLTAGG-VSVASLFMAGYLP 183 Query: 179 GLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTA 238 G+L+ +M +C I AK+R YP E +A K +AL L+ ++I++GGIL G+FTA Sbjct: 184 GILMGLAIMVVCAIIAKRRGYPVSERPTCAQAAKAFFDALPSLLLVIIVMGGILGGIFTA 243 Query: 239 TESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQI 298 TE++A+AVV++F +++ IYR+ KWRDLPKL+ +V SIV++LIGF+ + MT I Sbjct: 244 TEASAIAVVYTFILSVLIYREVKWRDLPKLILESVVMTSIVLLLIGFSVGMSWAMTNADI 303 Query: 299 PSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHF 358 P I+ A + +S+N VIL+ IN +L+++G MDM P +LI TPI LP+ +G+DPVHF Sbjct: 304 PYMISDALMGISENPVVILLLINIVLLIVGIFMDMTPAVLIFTPIFLPIAQDLGMDPVHF 363 Query: 359 GMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAIS 418 G++M+ NL IGL+TPPVG+ LFVG +I V I+ +K L+PFY AL + LM + YIP IS Sbjct: 364 GIMMVANLCIGLLTPPVGSALFVGCSISGVKIQQLIKPLLPFYAALLIALMMIVYIPQIS 423 Query: 419 LWLPSVV 425 L++P ++ Sbjct: 424 LFIPQLL 430 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: 609 Number of extensions: 33 Number of successful extensions: 4 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: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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