Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_044622617.1 H744_RS13655 C4-dicarboxylic acid transporter DauA
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000940995.1:WP_044622617.1 Length = 572 Score = 518 bits (1334), Expect = e-151 Identities = 258/502 (51%), Positives = 364/502 (72%), Gaps = 11/502 (2%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W+E ++ + D+++G+TVG++AIPL MALAI GV PQ+GLYT VAG++ AL GGSR Sbjct: 11 WREGFSLSSLRSDIVSGVTVGVVAIPLGMALAIAVGVPPQHGLYTVIVAGLLAALLGGSR 70 Query: 80 FSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGF 139 F+++GPTAAFVVIL P++QQ+GL+GL++AT++SG+ L+LMG+ R G+L+ Y+P VT GF Sbjct: 71 FNITGPTAAFVVILLPITQQYGLSGLMLATMMSGVILLLMGILRLGQLVAYVPYPVTTGF 130 Query: 140 TSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFW 199 T+GIG+TI +Q+KD LGL +A P H+ +KV A A+PT+N+ DA IG+VT+ + W Sbjct: 131 TAGIGLTIAFLQLKDLLGLSVASNPIHFPEKVVAYASAMPTLNMADALIGVVTIAAFILW 190 Query: 200 PRLGIRLPGHLPALLAGCAVMGIVNL-LGGHVATIGSQFHYVLADGSQGNGIPQLLPQLV 258 +L ++P H+ ALLAG + +VN GGHV +G +FHY + D G GIPQ+LPQLV Sbjct: 191 AKLKTKVPAHVVALLAGTLLALLVNHGSGGHVGLLGEKFHYQIGD-LVGQGIPQVLPQLV 249 Query: 259 LPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQG 318 +PW + +W + LLPAAF++AMLG IESLLCAVV DGMTGTKH N+ELVGQG Sbjct: 250 MPWQ----DGHFSWALVVELLPAAFTIAMLGCIESLLCAVVADGMTGTKHNPNAELVGQG 305 Query: 319 LGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSA 378 L N++ PFFGGI ATAAIAR+A N+RAGA SP+SA++HS+ V+ A++ LAP+LS++P+SA Sbjct: 306 LANMVVPFFGGIPATAAIARTATNIRAGAFSPLSAIVHSLFVLAAMIALAPMLSYVPMSA 365 Query: 379 MAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLF 438 +A LL+MVAWNMSEA V L+ AP+ D+ V+L C +LTV+FDMV+A+ VG++LA +LF Sbjct: 366 LAGLLIMVAWNMSEAPHFVHTLKVAPRRDVAVLLTCFTLTVVFDMVVAVVVGLLLAGVLF 425 Query: 439 MRRIARMTRLAPVVVDVP-----DDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILK 493 ++RIA +T + V P DDV+V + GPLFFAA+E + ++ + V+L Sbjct: 426 IQRIASLTTVDKVAGGHPHQNFGDDVVVYDINGPLFFAASEKALSVIDYTAPETQAVVLD 485 Query: 494 WDAVPVLDAGGLDAFQRFVKRL 515 + V +D + A + + R+ Sbjct: 486 FSDVTTIDITAIHALENAIDRI 507 Lambda K H 0.328 0.142 0.425 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: 772 Number of extensions: 36 Number of successful extensions: 5 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: 559 Length of database: 572 Length adjustment: 36 Effective length of query: 523 Effective length of database: 536 Effective search space: 280328 Effective search space used: 280328 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: 53 (25.0 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