GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Caulobacter crescentus NA1000

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate CCNA_01017 CCNA_01017 acyl-CoA synthetase

Query= metacyc::MONOMER-20125
         (556 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01017 CCNA_01017 acyl-CoA synthetase
          Length = 530

 Score =  216 bits (550), Expect = 2e-60
 Identities = 163/524 (31%), Positives = 252/524 (48%), Gaps = 45/524 (8%)

Query: 29  DCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAG 88
           D  +  ++    T++Q  R    +A+++ + G+  G  ++ +  N    +EL      AG
Sbjct: 26  DAVAFSFEGRETTFAQLDRHTNQVANALLAAGLSTGDRIAYVGKNSDHYFELLLGAAKAG 85

Query: 89  AILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLI--LEAIALFPKQAPVPRLVFMAD 146
            +   +  RL A  I+ ++  SE+KL+FV    R+LI  ++A+A      PV     +A 
Sbjct: 86  VVTTPIGWRLAAPEIAYIVGDSEAKLVFV---GRELIGHVDAVAAELTHRPV----VIAM 138

Query: 147 ESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCH 206
           E+E     +     F  ++D     DP      P    D  I  YTSGTT  PKG +  H
Sbjct: 139 EAEGAGDYQT----FEGWRDAASDVDPH----KPIQISDIAIQLYTSGTTGRPKGAMLTH 190

Query: 207 RGIFIMTVDSLID------WGVPKQPVYLWTLPMFHANGWSYPWGMAAV--GGTNICLRK 258
             +  M  ++  +      WG     V L  +P+ H  G    WG+  +  G   +  R+
Sbjct: 191 HNLLGMRREAAKNPLEWNQWG--PSDVSLVAMPVAHIGGTG--WGLVGLINGAKGVVARE 246

Query: 259 FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEPLKTT--VQIMTAGAPPPSAVLFRT 316
           FD   + D I++  ++ M   P  L ++   P +  +  +    I+   AP P  +L   
Sbjct: 247 FDPTKVLDFIEKDRISKMFMVPAALQIVVRLPRAREVDYSRLTHILYGAAPIPLDLLREC 306

Query: 317 -ESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQ-TKIDVVD 374
            E  G      YG+TET G VV   +    +H PA      K  +  G  M   ++ ++D
Sbjct: 307 MEVFGCGFVQQYGMTETTGTVV---YLPPEDHDPAGN----KRMRAAGLPMPGVELKIID 359

Query: 375 PVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLE 434
               A      +T+GEV +R  + M GY K  E TAK+M ADGW  TGD G +  DGYL 
Sbjct: 360 E---AGKSLPPNTVGEVAVRSSANMAGYWKLDEATAKTMDADGWLRTGDAGYLDEDGYLF 416

Query: 435 IKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTK 494
           I DR KD+IISGGEN+   EVES +Y HP + E AV+  PD+ WGE   A V+ K G+T 
Sbjct: 417 IHDRVKDMIISGGENIYPAEVESAVYGHPHVAEVAVIGVPDDKWGEAVKAVVAPKPGVT- 475

Query: 495 KPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILR 538
            P   +I+ + R+++  +  PK+V F   LP+ ++GK+ +  LR
Sbjct: 476 -PDADDIIAFARTRIAHFKAPKSVDFIPALPRNASGKILRRELR 518


Lambda     K      H
   0.319    0.135    0.412 

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: 772
Number of extensions: 41
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: 530
Length adjustment: 35
Effective length of query: 521
Effective length of database: 495
Effective search space:   257895
Effective search space used:   257895
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: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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