Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate Ac3H11_3520 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3520 Length = 426 Score = 303 bits (775), Expect = 9e-87 Identities = 160/420 (38%), Positives = 254/420 (60%), Gaps = 3/420 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDI-PLQAMMIQVASGVNKFSLLAIP 59 M FI LGS + + IG+P+AYAL +S W +D+ Q + V +G + F LLA+P Sbjct: 1 MTVFIFLGSLLAAMAIGVPIAYALLVSGAALMWHLDLFDAQILAQNVINGADSFPLLAVP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG IM GG+S+R+V A LVG RGGL V I+A+ A+SGS+VADTA++ + Sbjct: 61 FFMLAGEIMNVGGLSQRIVKLALTLVGHKRGGLGFVAILAACMLAALSGSAVADTAALAA 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +L+P M + G+ + + + S + A + PPS V++ +AA VSI+ LF+AGI+PG Sbjct: 121 LLLPMMVKAGHDKARAGGLIASAGIIAPVIPPSIGFVVFGVAAN--VSISKLFLAGIVPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 LL+ + +++ N E L+ E+ W L VI++ G+ GVFT T Sbjct: 179 LLMGVAIAVTWYWVSQRENVTPPPKASTAEKLQALKESTWALFLPVIVIVGLKMGVFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+AAVA V++ V +YR+ WR L + +T +++M L+ A +++T+ IP Sbjct: 239 EAAAVAAVYALLVATLVYRELHWRQLTDVFISAAKTTAVIMFLVAAAMVSAWLITVADIP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 ++ + L ++ ++L+ I ++M +GT MDM P ILILTP+L+PV+ G+DPV+FG Sbjct: 299 RQLVSLLKPLMEHPTLLLIAIMVLVMAVGTAMDMTPTILILTPVLMPVVKAAGIDPVYFG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 ++ ++N IGLITPPVG VL V + +GK+ ++ + ++PF A F ++ + P+I L Sbjct: 359 VLFIMNNAIGLITPPVGTVLNVVAGVGKMRMDEVTRGVIPFMAAQFAMMFLMVLFPSIVL 418 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: 522 Number of extensions: 25 Number of successful extensions: 3 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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