Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 3608435 Dshi_1832 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__Dino:3608435 Length = 446 Score = 301 bits (772), Expect = 2e-86 Identities = 155/440 (35%), Positives = 260/440 (59%), Gaps = 5/440 (1%) Query: 4 LIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPFFI 63 LI+FG + L+L G PI+++LG++ L + + PI V + FT + F +MA+P FI Sbjct: 7 LILFGGFLTLLLIGAPITVALGVSTLISFLYLGENPIKFVQIA-FTSVGSFPLMALPAFI 65 Query: 64 LAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVIL 123 LAG + G+++R+IN A + G + GG+ A V AC F A+SGS PAT A+G +++ Sbjct: 66 LAGALMEASGLSRRLINVAESFAGPFTGGMSAATVFACLFFGAISGSGPATTAAVGMLMI 125 Query: 124 PAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSS---AS 180 PAM+ +G+ + + + + +SG LGI+IPPSI ++++ +A GM + + S Sbjct: 126 PAMIQRGYGRSYSSAITASSGGLGIVIPPSIPLIIFGIAALGMPAPPEAVEKFGTFQTVS 185 Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYP-RLEKASLRQRWTAFREAAWGLMLIVV 239 + +LF+AG +P ++AG L + A+K GY E S RQ W W LM +V Sbjct: 186 IPKLFIAGFMPAFLIAGSLLLMNYILAKKHGYKGSAEGWSARQIWCELYRGFWALMAPLV 245 Query: 240 VIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNA 299 ++GGIY+G FTPTEAA ++ Y + +Y++L+ + + L ++ ++ +L I+ A Sbjct: 246 ILGGIYSGFFTPTEAAIVAIFYTLVVGTVIYRELSWQKLFTALETTTWLTGRVLLIMFTA 305 Query: 300 VLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFP 359 +F L+ IP + M++ + ++ +V + LL G FME + +LI+ P++ P Sbjct: 306 TVFGRLLVENQIPAVIANGMLSITDNIYIIWTLVILFLLFVGMFMETLATILILVPVMLP 365 Query: 360 VAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLA 419 VA +GIDP+HFG+++V + +G PP+G NL++ASGI+ + I ++VA P+ Sbjct: 366 VAYSVGIDPIHFGVVMVCCLGIGFQTPPLGENLFIASGISNISIERISVAALPFAFINTV 425 Query: 420 FLVLVTYVPAISLALPNLLG 439 + ++ +VP I+L LP LLG Sbjct: 426 AIFIIAFVPEITLWLPRLLG 445 Lambda K H 0.329 0.142 0.431 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: 647 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: 440 Length of database: 446 Length adjustment: 32 Effective length of query: 408 Effective length of database: 414 Effective search space: 168912 Effective search space used: 168912 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