Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate WP_057508017.1 ABB28_RS07385 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_014038 (428 letters) >NCBI__GCF_001431535.1:WP_057508017.1 Length = 447 Score = 507 bits (1306), Expect = e-148 Identities = 243/412 (58%), Positives = 327/412 (79%) Query: 6 FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 ++ LYFQV+ AI +G +LGH+ P +GE+MKPLGD F+ L+KMIIAPVIF T+VTGIAGM Sbjct: 17 YRQLYFQVVVAIILGAVLGHYEPLVGEKMKPLGDAFINLVKMIIAPVIFLTIVTGIAGMT 76 Query: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125 ++ VGR A A+ YF ST+AL++G+I+ +VVQPGAGMN++PA LD AV Y +++ Sbjct: 77 HLRTVGRVFAKAMAYFMFFSTLALVVGMIVAHVVQPGAGMNINPADLDQTAVNSYVEKSH 136 Query: 126 DQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 D ++ F MD+IP +++ AF GNILQVL AVLFG AL +G KG+ + N +E+ + Sbjct: 137 DLTLIGFAMDIIPKTLVSAFVDGNILQVLFVAVLFGIALALVGEKGKPVLNFLEALVAPV 196 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 F +++++M+ APIGAFGA+AFTIGKYGVG+L+ L L+ FY+T LFVV++LG++A+ Sbjct: 197 FKLVHILMKAAPIGAFGAIAFTIGKYGVGSLINLAWLVGSFYLTAFLFVVVILGAVARLC 256 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 GFS+FK RY++ ELL+VLGTSSSESALP +++KME+ GC KSVVGLV+PTGYSFNLDGT Sbjct: 257 GFSVFKLARYLKAELLLVLGTSSSESALPSLMEKMERAGCSKSVVGLVVPTGYSFNLDGT 316 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365 +IY+T+AA+FIAQATN+++ + HQI LL+V +LSSKGAAGVTG+GFI LAATL+ V +P Sbjct: 317 NIYMTLAALFIAQATNTELTLGHQIALLLVAMLSSKGAAGVTGAGFITLAATLAVVPEVP 376 Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNR 417 VAG+ALILG+DRFMSE R+LTN +GN VAT+VV++W LD +L L+ R Sbjct: 377 VAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWEGALDRDRLKLALDGR 428 Lambda K H 0.327 0.142 0.401 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: 602 Number of extensions: 23 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: 428 Length of database: 447 Length adjustment: 32 Effective length of query: 396 Effective length of database: 415 Effective search space: 164340 Effective search space used: 164340 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: 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