Aligments for a candidate for dauA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for dauA in Pseudomonas simiae WCS417

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate GFF25 PS417_00130 SulP family inorganic anion transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__WCS417:GFF25
          Length = 530

 Score =  209 bits (532), Expect = 2e-58
 Identities = 156/511 (30%), Positives = 258/511 (50%), Gaps = 53/511 (10%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + T A   RD + G++  ++A+P ++A A+ +G+ P+YGLY A +  ++  L G S 
Sbjct: 15  WLPRQTRASVGRDAMVGLSGAVLALPQSIAYALIAGLPPEYGLYAAIIPVLIACLWGSSW 74

Query: 80  FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131
             + GPTAA  ++LY        P SQ + +  +L+ T L+G+F  L+G+ RFG L+ ++
Sbjct: 75  HLICGPTAAISIVLYASVSPLAVPGSQDY-ITLILLLTFLAGVFQWLLGMLRFGALVNFV 133

Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQM---AHVPEHYLQKV---GALFMALPTINVGD 185
             SV LGFT G  + I   Q+ + LGL +   A    + L  +   G    A   + +G 
Sbjct: 134 SHSVVLGFTLGAAVVIALGQLPNLLGLDLPSQATAINNLLTLIHHSGEWDPASVILGLGT 193

Query: 186 AAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGS 245
             +G +   ++  WP L       L AL  G  V  +   + GHVA + S          
Sbjct: 194 LLVGALLKYLVPRWPTL-------LIALTLGSLVTWLWPAMFGHVALVSSF--------- 237

Query: 246 QGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTG 305
               I +L P   LP DL         D I  LLP+A ++ MLG + SL  A  L   + 
Sbjct: 238 ----IGKLPPLSPLPMDL---------DVILRLLPSAVAVGMLGLVTSLSIARSLSVRSQ 284

Query: 306 TKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALL 365
               AN E+  QG  NI+  FF G  +  +  RS  +  AGA SP++ V  ++ V L  L
Sbjct: 285 QLLDANQEIRAQGFSNIVGGFFSGYLSAGSFTRSGLSYEAGACSPLAGVFSALWVALFAL 344

Query: 366 VLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVI 425
             A L++ +P+ +MAA +L+++W + +   +  L R +  + +++ L C++ T+L ++  
Sbjct: 345 FGAALIAHIPIPSMAASILLISWGLVDRRGIRALFRVSRAEFVVMSLTCVA-TLLLELQT 403

Query: 426 AISVGIVLASLLFMRRIARMTRLAPVVVDVPD-DVLVLRVIGPLFFAAAEGLFTDLESRL 484
           AI  G++ +   +++R ++     P V    D D  VLRV G +FF A+  L   L+S L
Sbjct: 404 AIYAGVLASLFFYLKRTSQ-----PRVQQWRDGDEDVLRVGGSIFFGASHYLQVRLQS-L 457

Query: 485 EGKRIVILKWDAVPVLDAGGLDAFQRFVKRL 515
           +GKR+VI +   +  +D  G++   +  +RL
Sbjct: 458 QGKRVVI-EAQQINFIDYSGVEMLHQEARRL 487


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: 635
Number of extensions: 41
Number of successful extensions: 3
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: 530
Length adjustment: 35
Effective length of query: 524
Effective length of database: 495
Effective search space:   259380
Effective search space used:   259380
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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:

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, or view the source code.

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