GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Photobacterium gaetbulicola Gung47

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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