Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate WP_057508017.1 ABB28_RS07385 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q848I3 (444 letters) >NCBI__GCF_001431535.1:WP_057508017.1 Length = 447 Score = 494 bits (1272), Expect = e-144 Identities = 245/416 (58%), Positives = 326/416 (78%), Gaps = 2/416 (0%) Query: 6 PLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAG 65 P Y+ LYFQV+VAI +G +LGH+ P G +KPLGD FI L+KM+IAP+IF T+V+GIAG Sbjct: 15 PFYRQLYFQVVVAIILGAVLGHYEPLVGEKMKPLGDAFINLVKMIIAPVIFLTIVTGIAG 74 Query: 66 MQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTA 125 M ++++VG+ A+ YF ST+AL++G++V +VVQPG GM+I+ + LD + V +YV Sbjct: 75 MTHLRTVGRVFAKAMAYFMFFSTLALVVGMIVAHVVQPGAGMNINPADLDQTAVNSYVEK 134 Query: 126 GKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAH 185 D +++GF +++IP T+V AF +G+ILQVL +V+FG AL +G GKPVL+F++ Sbjct: 135 SHDLTLIGFAMDIIPKTLVSAFVDGNILQVLFVAVLFGIALALVGEKGKPVLNFLEALVA 194 Query: 186 VMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICR 245 +F +++++MK APIGA GA+AFTIG YGVGSL+ L L+ FY+T LFV+V+LGA+ R Sbjct: 195 PVFKLVHILMKAAPIGAFGAIAFTIGKYGVGSLINLAWLVGSFYLTAFLFVVVILGAVAR 254 Query: 246 AHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLD 305 GFSV KL RY++ ELL+VLGTSSSESALP ++ KMER G KSVVGLV+PTGYSFNLD Sbjct: 255 LCGFSVFKLARYLKAELLLVLGTSSSESALPSLMEKMERAGCSKSVVGLVVPTGYSFNLD 314 Query: 306 GTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGH 365 GT+IY+T+AA+FIAQAT+T + + HQI LLLV +LSSKGAAGVTG+GFI LAATL+ V Sbjct: 315 GTNIYMTLAALFIAQATNTELTLGHQIALLLVAMLSSKGAAGVTGAGFITLAATLAVVPE 374 Query: 366 LPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGR 421 +PVAG+ALILG+DRFMSE R+LTN +GNAVATVVV++W LD D+L +LA GR Sbjct: 375 VPVAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWEGALDRDRL--KLALDGR 428 Lambda K H 0.326 0.142 0.402 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: 597 Number of extensions: 21 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: 444 Length of database: 447 Length adjustment: 32 Effective length of query: 412 Effective length of database: 415 Effective search space: 170980 Effective search space used: 170980 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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