Align C4-dicarboxylate transporter, DctQ subunit (characterized)
to candidate SM_b20034 SM_b20034 ABC transporter
Query= reanno::psRCH2:GFF4196 (208 letters) >FitnessBrowser__Smeli:SM_b20034 Length = 187 Score = 54.3 bits (129), Expect = 1e-12 Identities = 54/188 (28%), Positives = 80/188 (42%), Gaps = 40/188 (21%) Query: 16 IAFLLAAMTLVTFVYVILNNLYTLFYNLGDRFEGSADFWFAIGDFIIGLAQAMTWSTALT 75 IA LLA+M ++ F V+L + Q +T S L+ Sbjct: 16 IALLLASMVVLVFGNVVLRYAFN---------------------------QGITVSEELS 48 Query: 76 KALFAWLIFSGLAYGVRTAGHIGVDALVKLAPRHIQRIIGIIACLLCLGYAGLL----TV 131 + F WL F G +R GH+GVD+L+K P + A +LC G+A +L V Sbjct: 49 RMFFVWLTFLGAVVAMREHGHLGVDSLIKRLPARAAK-----AAVLC-GHALMLYATWLV 102 Query: 132 ASFEWIQTLFIANIGAEDLGHIGVKQWHIGMIVPFGFAMVFIRFAEIF-VRILRNEQTGL 190 S W QTL ++GA G I + ++ G + FG I A+ F + R + T Sbjct: 103 ISGSWTQTLINLHVGAPATG-ISMAFFY-GAGLAFGIPAFLILLADAFAIATGRIDVTTT 160 Query: 191 GLADEAAD 198 L E+ D Sbjct: 161 DLVRESED 168 Lambda K H 0.331 0.145 0.465 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: 107 Number of extensions: 7 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: 208 Length of database: 187 Length adjustment: 20 Effective length of query: 188 Effective length of database: 167 Effective search space: 31396 Effective search space used: 31396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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