Aligments for a candidate for dauA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for dauA in Pseudomonas fluorescens GW456-L13

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate PfGW456L13_643 Sulfate permease

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_643
          Length = 522

 Score =  212 bits (539), Expect = 3e-59
 Identities = 158/504 (31%), Positives = 254/504 (50%), Gaps = 39/504 (7%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + T A   RDLI G++  I+A+P ++A A+ +G+ P+YGLY A +  ++  L G S 
Sbjct: 15  WLPRQTRASVGRDLIVGLSGAILALPQSIAYALIAGLPPEYGLYAAIIPVLIACLWGSSW 74

Query: 80  FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131
             + GPTAA  ++LY        P SQ + +  +L+ T L+GIF  L+GL RFG L+ ++
Sbjct: 75  HLICGPTAAISIVLYASVSPLAVPASQDYVML-ILLLTFLAGIFQWLLGLLRFGALVNFV 133

Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIV 191
             SV LGFT G  + I   Q+ + LGL +       L     L   L  ++    A+G+ 
Sbjct: 134 SHSVVLGFTLGAAVVIAIGQLPNLLGLDLPSQATA-LDSFITLLRHLGEMDKPSLALGLA 192

Query: 192 TLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIP 251
           T+ + V    L  R P  L  L+ G  ++ +   + GHV  + +                
Sbjct: 193 TVVVGVILKLLLPRWPTLLITLILGGLLVWLWPSMFGHVQLVSAF-------------TG 239

Query: 252 QLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKAN 311
           +L P   LP DL         D I  LLP+A ++ MLG + SL  A  +   +     AN
Sbjct: 240 KLPPFSPLPLDL---------DLILRLLPSAVAVGMLGLVTSLSIARSISARSQQLLDAN 290

Query: 312 SELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLL 371
            E+  QGL NI+  FF G  +  +  RS  +  AGA SP++ +  ++ V L  +  A L+
Sbjct: 291 QEVRAQGLSNIVGAFFSGSLSAGSFTRSGLSYEAGACSPLAGIFSALWVALFAIFGASLI 350

Query: 372 SWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGI 431
           + +P+ AMA  +L++AW + +   +  LLR +  + +++ L C++ T+L ++  AI  G 
Sbjct: 351 AHIPIPAMAGSILLIAWGLVDHRGIRALLRVSRAEFVVMALTCVA-TLLLELQTAIYAG- 408

Query: 432 VLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVI 491
           VLASL F  +     R+  V     D   +LRV G +FF A+  L   L+ R+ G R+VI
Sbjct: 409 VLASLFFYLKRTSQPRVQHVRDGEED---ILRVGGSIFFGASHYLQVRLQ-RMHGARVVI 464

Query: 492 LKWDAVPVLDAGGLDAFQRFVKRL 515
            +   +  +D  G++   +  +RL
Sbjct: 465 -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: 654
Number of extensions: 38
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: 522
Length adjustment: 35
Effective length of query: 524
Effective length of database: 487
Effective search space:   255188
Effective search space used:   255188
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.

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, 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