Alignments for a candidate for tctA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for tctA in Desulfovibrio vulgaris Miyazaki F

Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate 8501266 DvMF_1999 protein of unknown function DUF112 transmembrane (RefSeq)

Query= uniprot:E4PJQ9
         (508 letters)



>FitnessBrowser__Miya:8501266
          Length = 514

 Score =  307 bits (787), Expect = 5e-88
 Identities = 173/498 (34%), Positives = 286/498 (57%), Gaps = 8/498 (1%)

Query: 17  PYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPETAMILLTAVYAGAMYG 76
           P N++  + G   G ++G LPGL    GVA+++P  F +     + +I+L A+YAGA+YG
Sbjct: 15  PLNILLMVVGLTGGIIVGALPGLTATMGVALMVPATFAMDAT--SGLIMLGAIYAGAIYG 72

Query: 77  GRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASFAGGLIGTIGLIMLAPV 136
           G  S+ L+  PG   ++ T  DG+P+ Q GRA   L  S ++S  GG++GT+ L+ LA  
Sbjct: 73  GANSACLICTPGTPSSVATTFDGWPLCQAGRADIGLVTSLLSSAFGGIVGTVLLLFLAAP 132

Query: 137 LAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIMISTVGIDISTGTQRYT 196
           LA+FAL FG  E F L +   +T+  ++  N VK +++  +G+++STVGID + G  R+T
Sbjct: 133 LARFALQFGGPENFWLCIFGLSTIAVMSSGNMVKGLLSGAMGLLVSTVGIDPNAGVPRFT 192

Query: 197 FGVLELYEGIDFILAIVGLFAISELLFFVES-RMGRGRDKMNVGKLTLTMKELVMTIPT- 254
           FG   L +GI+ I A++GLF+ S++L+ + S +      +   G L   ++ LV      
Sbjct: 193 FGYYPLVQGIEVIPAMIGLFSFSQVLYLIGSYKPFIAEYQPTPGALGHVVRALVSRCKVI 252

Query: 255 QLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGDIRGVVAPEAGNNGASS 314
            LR  ++G + G+LPGAG  + S I+Y   K+      K+G+G + G+ + E+ NN    
Sbjct: 253 LLRSSLIGGLVGMLPGAGGEIASIIAYNESKRWDKDPSKYGKGAVEGLASSESANNAVIG 312

Query: 315 GALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWGVIAALLIGNVLLLVL 374
           G+L+PMLTLG+PGS   AV+L  L++  I PG  +FT   D+ +  I +    N+L++ +
Sbjct: 313 GSLIPMLTLGIPGSAVAAVILGALLAKGIQPGFKVFTTTGDLAYTFIMSQFAVNLLMIPV 372

Query: 375 NIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMVAFGVAGYFLRKLEIP 434
            + L     KLLSV   ++   + +++ +G Y+I +S  D++ ++AFG  GYF  ++ + 
Sbjct: 373 GLLLARVMTKLLSVRLTFVAIAIVVLSVIGSYAIRNSMLDVWIVIAFGFLGYFSGRVGLD 432

Query: 435 LVPIILGLLLGPEMEKNLGHALVLSDGEW----SVLWASPLAMGLWIVAGLGLILPYLVG 490
              + LG++LGP +E+NLG  + LS        +V   SP+A+ L+++  L L  P+L+ 
Sbjct: 433 TGAMALGIILGPMIEENLGKCVHLSRASGGSVINVFLESPIAILLFLMTMLSLATPFLLD 492

Query: 491 PLLRRRMNAAMKESPVSD 508
              +RR      E P  D
Sbjct: 493 WKRKRRDCGCDTEQPKED 510


Lambda     K      H
   0.325    0.144    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: 755
Number of extensions: 45
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: 508
Length of database: 514
Length adjustment: 35
Effective length of query: 473
Effective length of database: 479
Effective search space:   226567
Effective search space used:   226567
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources