Align C4-dicarboxylate TRAP transporter small permease protein DctQ (characterized)
to candidate GFF2913 PS417_14905 C4-dicarboxylate ABC transporter
Query= SwissProt::Q9HU17 (210 letters) >FitnessBrowser__WCS417:GFF2913 Length = 210 Score = 268 bits (684), Expect = 7e-77 Identities = 136/208 (65%), Positives = 157/208 (75%), Gaps = 1/208 (0%) Query: 1 MHALARVWARLEEGLIAFLLAAMTLVTFVYVVLNNLYTLLYDLADLWEGGNETLLAIGDG 60 M L RVW LEEG IAFLLAAMTLVTFVYV+LNN+YTL + LAD W ++ A+GD Sbjct: 1 MQTLRRVWEHLEEGFIAFLLAAMTLVTFVYVMLNNIYTLFFALADKWAWSSDFFGALGDH 60 Query: 61 VLTLAQEMTWSNALTKALFAWLIFLGIAYGVRTAGHLGVDVLVKLASRPVQRVLGVIACL 120 +T AQ+MTWS ALTKA+F WLIF GI+YGVRTAGHLGVD LVKL RPVQRVLG++ACL Sbjct: 61 TMTWAQDMTWSVALTKAMFGWLIFFGISYGVRTAGHLGVDALVKLTKRPVQRVLGMLACL 120 Query: 121 ACLGYAGLLCVASYDWVKTLFIAGIGAEDLDHFGIRQWHIGLIVPVGFALVFIRFAEILV 180 CL YAGL +ASY WV + A IGAEDLD +GI I +IVP+GFA+VFIR+ EI Sbjct: 121 CCLAYAGLFMIASYKWVTAVMGAHIGAEDLDQYGIDVGDIVVIVPIGFAMVFIRYLEIFY 180 Query: 181 RILRNRQTGLGLADEAADALKLT-EHEE 207 RI +RQ GLGLADEA +A KL HEE Sbjct: 181 RIFTHRQVGLGLADEAGEASKLAGSHEE 208 Lambda K H 0.328 0.143 0.442 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: 171 Number of extensions: 8 Number of successful extensions: 1 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: 210 Length of database: 210 Length adjustment: 21 Effective length of query: 189 Effective length of database: 189 Effective search space: 35721 Effective search space used: 35721 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 (21.7 bits) S2: 45 (21.9 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