GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_01017
          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 (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