GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Algiphilus aromaticivorans DG1253

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_043765768.1 U743_RS04305 long-chain-fatty-acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_000733765.1:WP_043765768.1
          Length = 513

 Score =  247 bits (630), Expect = 9e-70
 Identities = 159/518 (30%), Positives = 257/518 (49%), Gaps = 24/518 (4%)

Query: 28  LERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLE 87
           L RA +   D TA V  D R ++    D V   A A+   G  R D+++ +S N   ++E
Sbjct: 7   LRRAVQTRGDATATVCGDRRRSWREVADRVARLAGAVQALGVQRGDRVAILSLNSDRYIE 66

Query: 88  SFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKA--EII 145
             + V +AG    P+N R++P E+AY +  S S+ + VD+ +   L  +++Q+ A  ++I
Sbjct: 67  YLYAVAWAGAAANPVNIRMAPGEIAYTLEDSGSRVLFVDDTFAPMLPALREQVSALEQVI 126

Query: 146 LLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGV 205
              D + P  ++         +  L+   +  P+P     E  +  L+YT GTTG  KGV
Sbjct: 127 FCGDGELPEGTQG--------FEALI--AAHGPVPDADAGEEDLAGLFYTGGTTGKAKGV 176

Query: 206 MHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYP 265
           M  H     N +  +     D ++VYL   PMFH A    ++A  A G  +  + + D  
Sbjct: 177 MLSHDNVMHNMLNAIPILGYDASTVYLHAGPMFHLADMASTFAVTAAGGVHCVIPRFDIE 236

Query: 266 LIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPAT--LKAMQE 323
            +  ++++E+VTH    PT+   L    +      S+   ML  GA+P P    L+AM+ 
Sbjct: 237 PLLEIMQREKVTHTMLVPTMINMLLASGRIQEFDLSSLRRMLY-GASPMPEAVLLRAMEA 295

Query: 324 IGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKP 383
           +        G T+ YG                   +   A  G+P  S ++ + D +G  
Sbjct: 296 LP-----TTGFTQGYGQTEAAPLITFMPPEAHYAGSDKLASAGVPGYSVDVAIMDEDGTA 350

Query: 384 VPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKD 443
           +P     +GEV  RG N+  GY+K  E+TA + RDGW  +GD   +  DG++ IVDR KD
Sbjct: 351 LP--NGQVGEVCARGGNIMQGYWKRAEQTAATLRDGWLRTGDLGYMDDDGFVFIVDRAKD 408

Query: 444 LINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIK 503
           +I +GGE V S+ VE  + + P V+  AV G P E+WGE V A +  + G   TE+ +I+
Sbjct: 409 MIISGGENVFSVEVEGAIYQHPDVQETAVIGVPSERWGEAVHAVVVPKAGATPTEQAIIE 468

Query: 504 FCKERLAHFECPKIVEF--GPIPMTATGKMQKYVLRNE 539
            C+  +A ++ P+ VE    P+P++  GK+ K  LR++
Sbjct: 469 HCRGVIADYKLPRSVEIRSEPLPVSGAGKILKTTLRDD 506


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: 656
Number of extensions: 32
Number of successful extensions: 4
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: 513
Length adjustment: 35
Effective length of query: 514
Effective length of database: 478
Effective search space:   245692
Effective search space used:   245692
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 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