Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 3607680 Dshi_1089 TRAP dicarboxylate transporter- DctP subunit (RefSeq)
Query= SwissProt::P37735 (333 letters) >FitnessBrowser__Dino:3607680 Length = 330 Score = 123 bits (309), Expect = 6e-33 Identities = 95/316 (30%), Positives = 154/316 (48%), Gaps = 18/316 (5%) Query: 9 ALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYP 68 +++G+ AL+ +L P+ SH+ G+ FE+ E+ T GA+DVE+Y Sbjct: 13 SVIGSAALATEKMRISLQLPLT---SHL-------GENLQLFEKEVEERTGGAIDVEIYD 62 Query: 69 NSQLYKDKEELEALQLGAVQMLAPSLAKF-GPLGVQDFEVFDLPYIFKDYEALHK-VTQG 126 ++ LY+DKE A+ GA++ SL ++ G V D VF +P++F E + V +G Sbjct: 63 SATLYRDKEVPAAVGSGAIEAGVASLTQYVGDAPVVD--VFYMPFLFNTEEKVRAAVAEG 120 Query: 127 EAGKMLLSKLEAKGITGLAFWD--NGFKIMSANTPLTMPDDFLGLKMRIQSSKVLEAEMN 184 + +L AK + +W G ++S + P+ P+D G K R+ K L + Sbjct: 121 SPVREILETEIAKTGGEVLYWQAYGGAILLSQDEPIRTPEDMQGKKARV-FGKTLGDFVT 179 Query: 185 ALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVN 244 A G P +++ SE Y A Q G VD S + ++K+ EV T +NH + + V+VN Sbjct: 180 AAGGAPTLISGSEQYLAYQRGTVDVGMTGVSGVKSRKLWEVMDTITKTNHANIEFVVVVN 239 Query: 245 KQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAAW 304 +W+GL A+ + + A + D +A A ++ G T ELT EE A W Sbjct: 240 SDWWNGLDAETQGHINAAAQVAQDDVRDRMAAIEAEAYAAAEENGMT-IVELTDEELAKW 298 Query: 305 EEVLTPVHDEMAERIG 320 + V PV+D G Sbjct: 299 QAVSQPVYDSYLAATG 314 Lambda K H 0.314 0.130 0.364 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: 228 Number of extensions: 12 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: 333 Length of database: 330 Length adjustment: 28 Effective length of query: 305 Effective length of database: 302 Effective search space: 92110 Effective search space used: 92110 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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