Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 3607544 Dshi_0956 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Dino:3607544 Length = 428 Score = 321 bits (823), Expect = 2e-92 Identities = 167/425 (39%), Positives = 261/425 (61%), Gaps = 5/425 (1%) Query: 4 FILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVA--SGVNKFSLLAIPFF 61 +I+L +VL++ G+P+A+ LG++A + +D + +I + G N + L+A F Sbjct: 7 WIILILLVVLLIAGLPIAFVLGVTAAVMIL-LDPAVVPQIIGLIPFGGANNYLLVAALLF 65 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 ++AG IM +G ++ +L+AFA LVG +RGGL+ VNI+ S FF ISG++ +D A++GSV+ Sbjct: 66 MIAGEIMNQGKIAEKLIAFASSLVGHIRGGLAHVNILTSLFFSEISGTATSDAAAIGSVM 125 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 IP+M ++GYP F+ AVT + + A++ PPS N +LY+ A SIA LF AGI+PG L Sbjct: 126 IPQMRKRGYPAAFAAAVTSTSATMAIIVPPSLNLILYAYVANA--SIAELFAAGIVPGFL 183 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241 + ++MG I + KR YP + +A L +++L GIL G+FTATE+ Sbjct: 184 VCGLLMGTAYIISVKRGYPTEGAFSWGRVAETGKDAAIPLTLPILVLAGILGGIFTATEA 243 Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301 A+A WS + FIYR K L + + +++M ++ + G+ +T +IP Sbjct: 244 GAIAAFWSIVLAAFIYRTVKLGTLIDTLRIAGKRSAMLMFIVATSTLLGWYLTNQRIPQD 303 Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361 I L LSDN +VIL+ IN +L GT++ P IL+L PI LP+ +G+D VHFG+I Sbjct: 304 IAEGILGLSDNYWVILLAINVFFLLAGTIIHGTPAILMLVPIFLPLADQLGIDRVHFGLI 363 Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421 + +NLGIG TPPV +V+ + AI K+SI + +++ F A+ + L+ + PA+SLWL Sbjct: 364 LTINLGIGQQTPPVASVVLITCAIAKISIAKIIPSMLMFIGAMLVALLLINLFPALSLWL 423 Query: 422 PSVVL 426 PSV+L Sbjct: 424 PSVIL 428 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: 582 Number of extensions: 28 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: 428 Length adjustment: 32 Effective length of query: 394 Effective length of database: 396 Effective search space: 156024 Effective search space used: 156024 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