Alignments for a candidate for acs in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas litoralis 2SM5

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_090273988.1 BLU11_RS12930 fatty acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_900105005.1:WP_090273988.1
          Length = 560

 Score =  235 bits (600), Expect = 3e-66
 Identities = 164/535 (30%), Positives = 256/535 (47%), Gaps = 23/535 (4%)

Query: 23  TPLLF--LERAGKYFKDKTAVVYRD-SRYTYSTFYDNVMVQASALMRRGFSREDKLSFIS 79
           TPLL   L  +G  ++    +VYRD SRY Y+TF   +   A+ L   G    D ++ + 
Sbjct: 16  TPLLIKNLLLSGVRYEASQEIVYRDISRYDYATFNQRICRLANMLTNAGVKAGDTVAVLD 75

Query: 80  RNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQ 139
            +   +LE  F VP  G VL  +N RLSP+++ Y +NH+D   V+V+  +L     ++ Q
Sbjct: 76  WDSHRYLECMFAVPMIGAVLHTVNVRLSPEQIVYTMNHADDIMVLVNSEFLPLYQAIEPQ 135

Query: 140 IKA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSG 197
           +      ILL D    SA     +     Y +L+             +E S+ T +YT+G
Sbjct: 136 LTTVTTTILLTDDAVTSAE---LRGFAGEYEQLLAAAD-STYEFVDFDENSVATTFYTTG 191

Query: 198 TTGLPKGVMHHHRGAFLNAMAEV-------LEHQMDLNSVYLWTLPMFHAASWGFSWATV 250
           TTG PKGV   HR   L+ M +         E  M    VY+   PMFH  +WG  +   
Sbjct: 192 TTGNPKGVYFTHRQLVLHTMTQAGMLNGLGHEQMMSNRDVYMPITPMFHVHAWGMPYTAT 251

Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310
            +G   V   + +  L+ +L+++E+VT+    PT+   L +        F   + +++ G
Sbjct: 252 LLGVKQVYPGRYEPELLVKLIQQEKVTYSHCVPTILQMLLNAKTAEGYDFGG-MKIIIGG 310

Query: 311 AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYV 370
           +A      K     G  +   YG++ET    S      + ++   +EQ   K + GIP  
Sbjct: 311 SALTRGLYKTAGARGILLSGAYGMSETCPLISAGYNNLQIEAGSEDEQITHKIKAGIPVP 370

Query: 371 SFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVH 430
             E  + D  G  +P DG T GE+V+R   +  GY+K PEK+ E +  GW H+GD A + 
Sbjct: 371 LVEARLMDEQGNFLPHDGHTQGELVLRAPWLTQGYFKEPEKSRELWAHGWMHTGDVASID 430

Query: 431 PDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIEL 490
             G I+I DR KD+I TGGE +SS+ +E  +   P V+ VAV G PD +W E   A + +
Sbjct: 431 QAGSIDIRDRIKDVIKTGGEWLSSLELESLISLHPAVRDVAVVGVPDPRWDERPFALVVV 490

Query: 491 QEGVKLTEEEVIKFCKE-----RLAHFECP-KIVEFGPIPMTATGKMQKYVLRNE 539
             G ++   ++    +      R+  +  P +I     IP T+ GK+ K  +R E
Sbjct: 491 ASGEEMNATQLAAHLQPFVDDGRINKWAVPTQIAVVDEIPKTSVGKLDKKRIRVE 545


Lambda     K      H
   0.319    0.136    0.411 

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: 699
Number of extensions: 28
Number of successful extensions: 4
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: 549
Length of database: 560
Length adjustment: 36
Effective length of query: 513
Effective length of database: 524
Effective search space:   268812
Effective search space used:   268812
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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