Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate SM_b21353 SM_b21353 periplasmic C4-dicarboxylate transport protein
Query= SwissProt::Q9KQR9 (332 letters) >FitnessBrowser__Smeli:SM_b21353 Length = 325 Score = 132 bits (331), Expect = 2e-35 Identities = 93/317 (29%), Positives = 158/317 (49%), Gaps = 9/317 (2%) Query: 3 KPLTLIAASILAVTSFNAAANCDPGEIVIKFSHVTNTDKHPKGIAASLLEKRVNEEMNGK 62 K L +AA +L SF N + V++ S T+ D +P + V E G+ Sbjct: 2 KILVKLAAGLLVAASF--MGNAANAQTVLRSSD-THPDGYPTVEGVKYFGELVKERTAGR 58 Query: 63 ACMQVFPNSTLYDDDKVLEALLNGDVQLAAPSLSKFEKFTKKYRIFDLPFLFEDVDAVDR 122 ++V+ ++ L ++ +E + +G ++L S++ F K+ + LP+LF + + + Sbjct: 59 YSVEVYHSAQLGEEKDTIEQVRSGVIELNRVSMAPFNGTVKESIVPALPYLFRSEEHMHK 118 Query: 123 FQSSAKGEELKNAMTRRGVKGLEFWHNGMKQI-SANKPILVPADAKGLKFRVQASDVLVA 181 A G+++K A GV L F+ G + + KPI D KGLKFRV SD+ V Sbjct: 119 VMDGAIGDQIKKAFEGAGVVVLAFYDAGARSFYNKQKPINTVEDMKGLKFRVIQSDIFVD 178 Query: 182 QFEQIGANPQKMSFAETYGGLQTKVIDGQENTWSNIYGQKYFEVQDGTTETNHGILDYLV 241 +GAN M + E Y G++T VIDG EN + + K+FEV + H IL + Sbjct: 179 MVAALGANATPMPYGEVYSGIETGVIDGAENNFPSYDTAKHFEVAKNYSLDEHTILPEVF 238 Query: 242 VTSSKWWDGLPADVRDQFAKILNE-VTIERNAESNKVEELNKQYIIEAGGVVRTLTPEQR 300 V + +D L + ++ F + + V +R + KV+E + +EA G +T ++ Sbjct: 239 VMNKAAFDKLTPEDQEIFKQAAKDSVAKQRELWAAKVKESRAK--VEAAGA--KITTPEK 294 Query: 301 QQWVDALKPVWQKFEKD 317 Q ++DA+KPV++K D Sbjct: 295 QGFIDAMKPVYEKHVTD 311 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: 244 Number of extensions: 13 Number of successful extensions: 2 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: 325 Length adjustment: 28 Effective length of query: 304 Effective length of database: 297 Effective search space: 90288 Effective search space used: 90288 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