GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Marinobacter adhaerens HP15

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF1060 HP15_1039 acyl-CoA synthetase

Query= BRENDA::A4YDR9
         (549 letters)



>lcl|FitnessBrowser__Marino:GFF1060 HP15_1039 acyl-CoA synthetase
          Length = 542

 Score =  430 bits (1106), Expect = e-125
 Identities = 224/535 (41%), Positives = 328/535 (61%), Gaps = 5/535 (0%)

Query: 10  EGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGF 69
           +G+ P  + Y+V +P+ F+ER    + +  AV++   RY ++  Y+     ASAL  RG 
Sbjct: 7   QGLAPVDANYAVQSPVDFIERTATVYPEYPAVIHGAIRYNWAQTYERCRRLASALKGRGI 66

Query: 70  SREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY 129
            R D ++ +  N P  +E+ FGVP  G VL  +N RL  + +A++++H ++K V+ D  +
Sbjct: 67  GRGDTVAVMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVIADREF 126

Query: 130 LNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSM 189
              + +   ++  + +++ D D+P   E  +    + Y   ++ G         + E+  
Sbjct: 127 GEVIRDAVSRLDTKPLVI-DVDDPEYGEGVQVS-DLDYEAFLQEGDPTFQWSFPENEWDA 184

Query: 190 ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWAT 249
           I+L YTSGTTG PKGV++HHRGA++NA+       MD++ VYLWTLPMFH   W F W  
Sbjct: 185 ISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVWSMDMHPVYLWTLPMFHCNGWCFPWTI 244

Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309
            A+  T+VCL +VD   I +L+   +VTHMC AP V   L +  +       + V  + A
Sbjct: 245 TAMAGTHVCLRRVDPEKILQLIRDHQVTHMCGAPIVLNALLNVPESAKAGIDHDVKSMTA 304

Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369
           GAAP    + A++E+G  + HVYGLTE YGP ++C W+ EWD+LPL ++A+ KARQG+ Y
Sbjct: 305 GAAPPAQVIGAIEEMGIQVTHVYGLTEVYGPVTVCAWKSEWDALPLHDRARKKARQGVRY 364

Query: 370 VSFE-MDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427
            +     V D N  +PVP DGKTIGE+ +RG+ V  GY KNP+ T E+FR GWFH+GD A
Sbjct: 365 HTLAGTMVGDPNTMEPVPKDGKTIGEIFLRGNTVMKGYLKNPKATEEAFRGGWFHTGDLA 424

Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487
           V H DGY+EI DR KD+I +GGE +S+I VE TL   P V   AV   PDEKWGE   A 
Sbjct: 425 VWHEDGYMEIKDRLKDIIISGGENISTIEVEDTLYRHPAVLEAAVVARPDEKWGETPCAF 484

Query: 488 IELQ-EGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541
           + L+ E   ++EE++I FC+E LA F+ PK + F  +P T+TGK+QK+VLR++AK
Sbjct: 485 VTLKPEAGDVSEEDIINFCREHLARFKVPKTIVFSELPKTSTGKIQKFVLRDQAK 539


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: 802
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: 542
Length adjustment: 35
Effective length of query: 514
Effective length of database: 507
Effective search space:   260598
Effective search space used:   260598
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