Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate AZOBR_RS26625 AZOBR_RS26625 dehydroascorbate transporter
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__azobra:AZOBR_RS26625 Length = 427 Score = 306 bits (785), Expect = 6e-88 Identities = 157/414 (37%), Positives = 259/414 (62%), Gaps = 3/414 (0%) Query: 5 ILLGSFIVLILIGMPVAYALGLSAL-IGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFVL 63 I +GS + + +G+P+A+AL +S L + A+ + Q ++ + G N F LLA+PFF+L Sbjct: 5 IFVGSLLGAMALGLPIAFALIVSGLALMAFMGMLDPQIVVQSMWDGANSFPLLAVPFFML 64 Query: 64 AGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIP 123 AG M GGMSRR++A A VG +RGGL V + A+ ++SGS+VADTA++ S+L+P Sbjct: 65 AGEFMNAGGMSRRIIAMAMAWVGHLRGGLGFVAVFAAILMASLSGSAVADTAALASILLP 124 Query: 124 EMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLS 183 M + GY S + +G + A + PPS +LY +A G VSI LF+AGI+PG+++ Sbjct: 125 MMRQAGYDIHRSGGLIAAGGIIAPVIPPSIGMILYGVA--GQVSITKLFLAGIVPGIMMG 182 Query: 184 AVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAA 243 ++ A++ +PLRE L++ +A W ++ V+I+GG+ +GVFT TE+A Sbjct: 183 VALLITWWWLARREILTTPPKVPLRERLRLTADAFWAMLLPVVIIGGLKTGVFTPTEAAV 242 Query: 244 VAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKIT 303 VA V++ FV + IYR+ + DL LM +T ++VM L+ A +++T IP+++ Sbjct: 243 VAAVYAMFVGLVIYRELRIADLYGLMLSAAKTTAVVMFLVAAAGISAWLITASNIPAQLA 302 Query: 304 TAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIML 363 + DNR ++++ + +++++GT +D AP IL++ P+L+P+I G+DPV+FG++ + Sbjct: 303 DLLAPVMDNRLLLMLALMVIVLIVGTALDFAPTILLMVPVLMPIIKQAGIDPVYFGVLFI 362 Query: 364 VNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAI 417 +N IGLITPPVG VL V +G++S+ + +K + PF LA VL + P + Sbjct: 363 MNNAIGLITPPVGTVLNVVCGVGRMSMSNLMKGVGPFLLAQTAVLFLLVLFPEL 416 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: 583 Number of extensions: 39 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