Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate AZOBR_RS09595 AZOBR_RS09595 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__azobra:AZOBR_RS09595 Length = 432 Score = 331 bits (848), Expect = 3e-95 Identities = 165/426 (38%), Positives = 266/426 (62%), Gaps = 4/426 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWID-IPLQAMMIQVASGVNKFSLLAIP 59 M A I+ G +VL+L GMP++ +LGL+ L + + +P++A+ +++ +G+ KF ++AIP Sbjct: 1 MNAAIIFGLLLVLMLTGMPISISLGLTVLTFLFTMTHVPIEAVALKLFTGIEKFEIMAIP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG + GG++RR++ FA +VG GGL L +M F A+SGSS A ++GS Sbjct: 61 FFILAGNFLTHGGVARRMINFATAMVGHWHGGLGLAGVMGCALFAAVSGSSPATVVAIGS 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIAS---LFMAGI 176 +++P M +G+P++F V + +L PPS V+Y +A GT + AS LFMAG+ Sbjct: 121 IVLPAMVAQGFPKQFGAGVITTSGALGILIPPSIVMVMYCVATSGTANSASVGQLFMAGV 180 Query: 177 MPGLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVF 236 +PGL+L+ V+ G+ A+K YP+ L E K EA+WGL +VI++GGI SGVF Sbjct: 181 IPGLMLAFVLGGVTWYRARKFGYPRLPKASLGERFKAFREAIWGLSLIVIVIGGIYSGVF 240 Query: 237 TATESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLM 296 T TE+AA++ V++F + +F+Y+D R +PK++ + ++++ +I A F +V+T Sbjct: 241 TPTEAAAMSAVYAFIIAVFVYKDMPLRGVPKVLLSSASMSAMLLYIITNAVLFSFVLTSE 300 Query: 297 QIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPV 356 IP I + L+ N +L++ G M+ + ++LI+ PIL PV +G+DPV Sbjct: 301 NIPQAIADWIVNQGLGVIAFLLVTNILLLMAGNFMEPSSIVLIMAPILFPVAMKLGIDPV 360 Query: 357 HFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPA 416 HFG++M+VN+ +G+ PPVG L+V S I K+ I A+ P+ LA+ L+ +TY+P Sbjct: 361 HFGIMMVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLAMLGFLVLITYVPI 420 Query: 417 ISLWLP 422 IS WLP Sbjct: 421 ISTWLP 426 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: 595 Number of extensions: 39 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: 432 Length adjustment: 32 Effective length of query: 394 Effective length of database: 400 Effective search space: 157600 Effective search space used: 157600 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