Alignments for a candidate for paaK in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Pseudomonas stutzeri A1501

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011911355.1 PST_RS00545 long-chain fatty acid--CoA ligase

Query= BRENDA::D3GE78
         (556 letters)



>NCBI__GCF_000013785.1:WP_011911355.1
          Length = 539

 Score =  192 bits (488), Expect = 3e-53
 Identities = 157/515 (30%), Positives = 239/515 (46%), Gaps = 36/515 (6%)

Query: 46  LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104
           L+  DL   +   A  LR  +GLQ GDR+ L   N L +P+   G + AG +    NP +
Sbjct: 45  LSYADLARQADAFARYLRHHAGLQPGDRLALQLPNSLQYPIATFGALKAGLVIVNTNPQY 104

Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCA 164
            A E  +Q +DSGA  +L     L   L  A QA      I    TS+ D      +   
Sbjct: 105 TAAEARHQFRDSGARAILVLDRLLP--LVRAVQADTALERIIL--TSVED-----LQAPV 155

Query: 165 YWSDLLASEEEGAAFTWDELSTPALSSTT-----LALNYSSGTTGRPKGVEISHRNYVAN 219
           Y S   A+E    A    E S PAL           L Y+ GTTG  KG  +SHRN +AN
Sbjct: 156 YDSLEPATERFMQALRLGEQS-PALDCVVGLERLALLQYTGGTTGVSKGAMLSHRNLLAN 214

Query: 220 MLQ----YCHTASLHPDYKARLERSRWLCFLPMYHAMA--QNIFIAAALYRATPVYIMSK 273
           +LQ    +     L P+   R+        LP+YH MA   N   +  +   T V+I   
Sbjct: 215 VLQTIELFDKPGLLEPEKDVRIAP------LPLYHIMAFATNCLSSVGMGLHT-VFIRDG 267

Query: 274 FDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEV 333
            +  + +   QR   +    +  + V L  HP     D S ++   SG APL  EV    
Sbjct: 268 RNLDETIGAMQRHPFSLLSGINTLFVGLMNHPQFRSIDFSHLKWATSGGAPLNSEVGRRW 327

Query: 334 EKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGVEVKERN 393
           + L       I++G+G+TEA+  V             +G+   + E + + D        
Sbjct: 328 QVLTGAP---IREGFGLTEASPVVATGTALSPYREGYIGQALIDTELRTVDDDGNDVPAE 384

Query: 394 SRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVK 453
           S GELW+R P VM+GYW+  + T +  T DGWL TGDIA +D +G   +VDR K++I V 
Sbjct: 385 SPGELWLRGPQVMQGYWQRPEETAKVITADGWLKTGDIALLDAEGFVKIVDRKKDMILVS 444

Query: 454 GNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIAHYLDNK 512
           G  V P E+E +L++HP++ +   +G+      E  + +V LR  ++     +  +    
Sbjct: 445 GFNVFPNEIEDVLMQHPSVRECVAVGIPDARKGEAVKVFVSLR--EATDDQALLEHCRQF 502

Query: 513 VSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAK 547
           ++ +K +   +   + +PK   GK+LR +LR++A+
Sbjct: 503 LTGYK-LPSAIEIRDELPKTAVGKLLRRQLRDEAR 536


Lambda     K      H
   0.319    0.134    0.403 

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: 621
Number of extensions: 26
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: 556
Length of database: 539
Length adjustment: 36
Effective length of query: 520
Effective length of database: 503
Effective search space:   261560
Effective search space used:   261560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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:

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