Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 3607546 Dshi_0958 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= SwissProt::Q9KQR9 (332 letters) >FitnessBrowser__Dino:3607546 Length = 326 Score = 120 bits (300), Expect = 6e-32 Identities = 77/216 (35%), Positives = 109/216 (50%), Gaps = 2/216 (0%) Query: 52 EKRVNEEMNGKACMQVFPNSTLYDDDKVLEALLNGDVQLAAPSLSKFEKFTKKYRIFDLP 111 E+R+ G+ +Q+F ++TL ++ VL+ L G Q A+ S S + + IFDLP Sbjct: 47 EQRLEAAAPGEIDVQIFMSNTLGKEEDVLQGLGFGTHQ-ASLSASAVAQVNNRTSIFDLP 105 Query: 112 FLFEDVDAVDRFQSSAKGEELKNAMTRRGVKGLEFWHNGMKQISAN-KPILVPADAKGLK 170 +LFED AV F S GE L + G+ W NG +QI+ N +PI+ PAD GLK Sbjct: 106 YLFEDRAAVQTFIDSPAGEMLADGFDVTGMVLAAMWDNGFRQITNNVRPIVTPADLDGLK 165 Query: 171 FRVQASDVLVAQFEQIGANPQKMSFAETYGGLQTKVIDGQENTWSNIYGQKYFEVQDGTT 230 R + V F +GAN +SF E Y L IDGQEN + + K FEVQ + Sbjct: 166 IRTPTNRQRVEMFNTLGANATPLSFGEVYSALDQGTIDGQENPANVVETAKLFEVQGYMS 225 Query: 231 ETNHGILDYLVVTSSKWWDGLPADVRDQFAKILNEV 266 TNH L V + + L ++R+ + EV Sbjct: 226 LTNHVYLPTFFVIGEPFLNSLTPELRETVISVAKEV 261 Lambda K H 0.316 0.132 0.383 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: 229 Number of extensions: 17 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: 332 Length of database: 326 Length adjustment: 28 Effective length of query: 304 Effective length of database: 298 Effective search space: 90592 Effective search space used: 90592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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