GapMind for catabolism of small carbon sources

 

Alignments 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.

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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:

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:

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:

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:

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