Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 206131 DVU0705 TRAP dicarboxylate transporter, putative
Query= uniprot:Q88NP0 (426 letters) >MicrobesOnline__882:206131 Length = 427 Score = 260 bits (664), Expect = 6e-74 Identities = 149/419 (35%), Positives = 236/419 (56%), Gaps = 2/419 (0%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFVLA 64 +L G F V++ IG+P+A A+GLSA + + L ++ I V +GV K+ LLAIP F+ A Sbjct: 4 LLFGLFAVMMFIGVPLATAMGLSATVAIAAAKLGLLSVPISVYTGVAKYPLLAIPMFIFA 63 Query: 65 GAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPE 124 G + G++ RLV F LVG +RGGL++ +IM G ISGS AD A+V V+IP Sbjct: 64 GMVFERSGVALRLVNFTVALVGPLRGGLAIASIMVCMVLGGISGSGPADAAAVAMVMIPG 123 Query: 125 MERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSA 184 M GYP+ FS + + A+L PPS +LYS+ S+ +LF AG++PG L Sbjct: 124 MAAAGYPKAFSAGLIAAAGSTAILIPPSIAFILYSVLVP-QASVPALFAAGLIPGFLAGI 182 Query: 185 VMMGLCLIFAKKRNYPK-GEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAA 243 ++ + + + G+ L EA+WGL+A VIILGGI SG FT TE+A Sbjct: 183 ALIIPAWALSVRHGFGLVGDDASCGSILIAFKEAIWGLLAPVIILGGIRSGYFTPTEAAV 242 Query: 244 VAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKIT 303 AV + FV F+YR R + +L+ + ++VM++I ++ F + + + + Sbjct: 243 AAVFYGLFVGFFVYRTLTLRGIYELLVESAEVSAVVMMIIALSSVFAWAGSTLGAFEAMG 302 Query: 304 TAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIML 363 A + +S + + L+ + +L++ G +D ++ I PILLPV+T G + V FG+IM Sbjct: 303 NALIGISTSETMTLLAVVLVLIIAGMFLDGVSILFIFIPILLPVMTHFGWNAVWFGVIMT 362 Query: 364 VNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWLP 422 + L IG TPP+ L V + I + IE TV ++ F LA+ + ++ V ++P ++ +P Sbjct: 363 MCLAIGQFTPPLALNLMVTTRIADIGIEETVPWVLWFVLAMTIAMLLVVFVPQLATLVP 421 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: 576 Number of extensions: 34 Number of successful extensions: 4 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