Aligments for a candidate for acs in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Pseudomonas stutzeri RCH2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF2177 Psest_2220 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__psRCH2:GFF2177
          Length = 585

 Score =  493 bits (1269), Expect = e-144
 Identities = 267/561 (47%), Positives = 353/561 (62%), Gaps = 18/561 (3%)

Query: 25  FDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEK-YTFKEMKEES 83
           F W  A    +    G LN A+EA+DRHA   R    AL + +     +  ++ ++K ++
Sbjct: 29  FSWPMAADALNGLPGGGLNLAHEAVDRHAAGPRAGYCALRFLERNGSRRELSYLQLKRQT 88

Query: 84  NRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLE 143
           NR  NVL + G V +G+R+F+   R  ELY  +LG +K G +  PLF AF    ++ RL 
Sbjct: 89  NRFANVLAQLG-VARGERLFVLCNRGVELYLGVLGGLKNGCVVSPLFAAFGPEPLETRLR 147

Query: 144 NSEAKVVVTTPELLERIPV----DKLPHLQHVFVV----GGEAESGTNIINYDEAAKQES 195
             +  V++T+ E+L R  V    D+LP L+HV +     G  +  GT  ++   AA  E 
Sbjct: 148 LGDCSVLLTS-EMLYRKKVARLRDRLPLLKHVLLYDESGGHTSIDGTLDLHDLLAAAGEE 206

Query: 196 TRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWCTAD 255
            ++     D     LLH+TSG+TGTPKG LHVH A +  Y TG++ LDL  +DIYWC+AD
Sbjct: 207 FKIAPTTADSPS--LLHFTSGTTGTPKGALHVHGAALTHYVTGRYALDLHPDDIYWCSAD 264

Query: 256 PGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGD 315
           PGWVTGT YGI AP L G T+V+  G F  E WYG +E+  ++VWY+APTA RMLM AG 
Sbjct: 265 PGWVTGTSYGILAPLLLGVTSVVDCGEFDAERWYGILEKERISVWYTAPTAIRMLMKAGP 324

Query: 316 EMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIK 375
           E+A ++    LR V SVGEPLNPE + WG +V    IHD WW TETG  +I N P M IK
Sbjct: 325 ELARRHFHPQLRFVASVGEPLNPEAVWWGKEVLGLPIHDNWWQTETGGIMIANIPAMPIK 384

Query: 376 PGSMGKPIPGVEAAIV----DNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFM 431
           PGSMGKP+PGVEAAIV    D     L    +G LA+K+ WP M  T     E+Y   F 
Sbjct: 385 PGSMGKPLPGVEAAIVRHGEDGNLTFLGDDEIGELALKQPWPGMFRTYLGQEERYRRCF- 443

Query: 432 PGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKP 491
            G WY+SGD A  D +GY+WF GR DDVI ++G  +GPFEVES L+EH A+AEA VIGKP
Sbjct: 444 AGDWYLSGDLARRDADGYYWFIGRSDDVIKSAGHLIGPFEVESALMEHSAVAEAAVIGKP 503

Query: 492 DPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIM 551
           DP+ GE +KAF++L+ G E S+ L +E+    ++ L A  AP+E+EF   LP+TRSGK+M
Sbjct: 504 DPLLGETVKAFVSLKRGREASEALHDELIGHARKRLGAAVAPKELEFLASLPRTRSGKLM 563

Query: 552 RRVLKAWELNLPAGDLSTMED 572
           RR+LKA EL LP GD+ST+E+
Sbjct: 564 RRLLKARELGLPEGDISTLEN 584


Lambda     K      H
   0.318    0.136    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: 1015
Number of extensions: 52
Number of successful extensions: 6
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: 572
Length of database: 585
Length adjustment: 36
Effective length of query: 536
Effective length of database: 549
Effective search space:   294264
Effective search space used:   294264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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