GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium grahamii CCGE 502

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_016554064.1 RGCCGE502_RS10110 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_000298315.2:WP_016554064.1
          Length = 362

 Score =  148 bits (373), Expect = 4e-40
 Identities = 115/373 (30%), Positives = 194/373 (52%), Gaps = 36/373 (9%)

Query: 194 YTSGTTGLPKGVMHHHRGAFLNAMA-EVLEHQMDLNSVYLWTLP------------MFHA 240
           YT+G+TGLPKG ++ H GAFL ++    +   +D ++ +L T+P            +FHA
Sbjct: 4   YTTGSTGLPKGAVYPH-GAFLQSILYTAMLEGIDPSTRWLHTMPAAGVPLMHMIRNLFHA 62

Query: 241 ASWGFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLAD--YMKRNNL 298
           A      ATV VG  +      +  L   L+ +E  T++   PT+  +L +   ++R ++
Sbjct: 63  A------ATVIVGPWSA-----EQALF--LIGREHTTNVVLVPTMLNSLLESSMLERTDM 109

Query: 299 KFSNRVHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQ 358
             S R+    A + P     KAM+        ++G TE  G  S+  +  + + L +  +
Sbjct: 110 S-SMRLFGYGASSLPPKTIKKAMKAFDRPFLQMFGTTELMGM-SMMLFPSDHE-LGITTR 166

Query: 359 AKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRD 418
            ++    G P    ++ V D +G+ +P  G+T GE+++R      GY+  PEK+AE  +D
Sbjct: 167 PEILGSAGKPLPFVDVKVVDGDGRSLP-SGET-GELIVRSDTQFSGYWNAPEKSAEVIKD 224

Query: 419 GWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDE 478
           GW ++GD A     GY+ + DR K  I +GG  V    VE  L E P +  VAV G PDE
Sbjct: 225 GWIYTGDLASRDEAGYVYLSDRAKFRIRSGGYDVFPTEVENALAEHPAISEVAVIGLPDE 284

Query: 479 KWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVE-FGPIPMTATGKMQK-YVL 536
           ++GE + A +    G  +T +E+ +FC+ ++A F+ PK ++ +  IP   TGK+QK  ++
Sbjct: 285 RYGERIHAVVTTVPGKTVTSDELREFCRNKIAAFKVPKRIDIWTEIPKGPTGKIQKRAII 344

Query: 537 RNEAKAKANKEKS 549
            + A   A+++ S
Sbjct: 345 EHFASEAASRQAS 357


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: 448
Number of extensions: 21
Number of successful extensions: 2
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: 362
Length adjustment: 32
Effective length of query: 517
Effective length of database: 330
Effective search space:   170610
Effective search space used:   170610
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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