Align TRAP-type large permease component (characterized, see rationale)
to candidate BWI76_RS24135 BWI76_RS24135 c4-dicarboxylate permease
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Koxy:BWI76_RS24135 Length = 433 Score = 291 bits (744), Expect = 3e-83 Identities = 153/404 (37%), Positives = 247/404 (61%), Gaps = 3/404 (0%) Query: 16 IGVPVAFSLMFCGVVLMWYMGMFNTQII--AQNMIAGADTFTLLAIPFFILAGELMNAGG 73 IGVP++FS+ V M M ++ +I +Q + G D F LLAIPFFI AG LMN+GG Sbjct: 19 IGVPISFSIGIATVGSMLLMFPWDIAVITVSQRLANGLDNFALLAIPFFIFAGTLMNSGG 78 Query: 74 LSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKAGYNV 133 ++ R+I+ A VG + G LG V ++A ++ SISGSA A AA+ L P+ + GY+ Sbjct: 79 IAIRLINLAQVMVGRVPGSLGHVNVLANMMFGSISGSAVAAAAAVGGTLNPIQTRKGYDP 138 Query: 134 PRSAGLIAAGGVIAPVIPPSMAFIVFGVAAN-VSITQLFMAGIVPGLIMGIALVATWLLV 192 S + + + +IPPS IVF + A VS+ LFMAG +PG++MG+A++ ++ Sbjct: 139 AFSTAVNVSSCITGLLIPPSNVLIVFSLTAGGVSVASLFMAGYLPGILMGLAIMVVCAII 198 Query: 193 VRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVAAVYALFVG 252 ++ R + A AL +L + +I++GGI G+ T TEA+ +A VY + Sbjct: 199 AKRRGYPVSERPTCAQAAKAFFDALPSLLLVIIVMGGILGGIFTATEASAIAVVYTFILS 258 Query: 253 MVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLIDRP 312 ++IYRE+K RDLP +IL++ T++++ L+ ++ SW +T A+IP I+ + + + P Sbjct: 259 VLIYREVKWRDLPKLILESVVMTSIVLLLIGFSVGMSWAMTNADIPYMISDALMGISENP 318 Query: 313 TLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGLLTP 372 +++ +I +V+L+VG +D+TP +LI TP+ +PI + G+DPV+FG++ + N CIGLLTP Sbjct: 319 VVILLLINIVLLIVGIFMDMTPAVLIFTPIFLPIAQDLGMDPVHFGIMMVANLCIGLLTP 378 Query: 373 PVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 PVG L V + V + ++I + PF A ++ L ++V P I Sbjct: 379 PVGSALFVGCSISGVKIQQLIKPLLPFYAALLIALMMIVYIPQI 422 Lambda K H 0.331 0.145 0.430 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: 454 Number of extensions: 24 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 433 Length adjustment: 32 Effective length of query: 393 Effective length of database: 401 Effective search space: 157593 Effective search space used: 157593 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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