Align C4-dicarboxylate TRAP transporter small permease protein DctQ (characterized)
to candidate AZOBR_RS09600 AZOBR_RS09600 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07837 (227 letters) >FitnessBrowser__azobra:AZOBR_RS09600 Length = 226 Score = 228 bits (582), Expect = 6e-65 Identities = 112/200 (56%), Positives = 138/200 (69%), Gaps = 24/200 (12%) Query: 2 LRILDRAEEVLIAALIATATVLIFVSVTHRFTLGF--VADFVGFFRGHGMTGAAAAAKSL 59 ++ILD EE+LIA L+A AT +IF+SV HR+ GF + D++ + Sbjct: 1 MKILDHLEEILIAFLMAAATTIIFISVAHRYAAGFPIIQDYILHW--------------- 45 Query: 60 YTTLRGINLVWAQELCIILFVWMAKFGAAYGVRTGIHVGIDVLINRLDAPKRRFFILLGL 119 NL WAQELCI +FVWMAKFGAAYGVRTGIHVG+DVLIN+L P R FI+ GL Sbjct: 46 -------NLAWAQELCIYMFVWMAKFGAAYGVRTGIHVGVDVLINKLSTPLRAKFIVFGL 98 Query: 120 GAGALFTGIIATLGANFVLHMYHASSTSPDLELPMWLVYLAIPMGSSLMCFRFLQVAFGF 179 AGA FTG++ T+G+ FV HM S DLE PMW++YLAIP+GS LMCFRFLQV F Sbjct: 99 LAGATFTGVVGTMGSTFVWHMSDTEQVSADLEWPMWIIYLAIPLGSYLMCFRFLQVMVNF 158 Query: 180 ARTGELPHHDHGHVDGVDTE 199 RTGELPHHDHGHV+G++ + Sbjct: 159 LRTGELPHHDHGHVEGLEED 178 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: 164 Number of extensions: 9 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: 227 Length of database: 226 Length adjustment: 22 Effective length of query: 205 Effective length of database: 204 Effective search space: 41820 Effective search space used: 41820 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: 46 (22.3 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