GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Nocardioides daejeonensis MJ31

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_110205235.1 DNK54_RS01815 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_003194585.1:WP_110205235.1
          Length = 510

 Score =  303 bits (777), Expect = 8e-87
 Identities = 194/522 (37%), Positives = 270/522 (51%), Gaps = 44/522 (8%)

Query: 27  FLERAGKYFKDKTAVVYRDSR-------YTYSTFYDNVMVQASALMRRGFSREDKLSFIS 79
           F+ RA   + D+  V+    +        TY   ++     A+ L   G    D+++ +S
Sbjct: 10  FVNRAATVYGDRIGVIDEPDQPAPSLGSLTYREMHERAARMAARLDELGIGVGDRVAVVS 69

Query: 80  RNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQ 139
            N    L +FFGV   G VLVP+NFRL P E+AYII HS ++ + VD     +L EV  +
Sbjct: 70  HNSARLLTAFFGVAGYGRVLVPVNFRLRPDEVAYIIEHSGARVLYVDPELDEALAEVTAE 129

Query: 140 IKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTT 199
            +  +   E+   P  +E    E                      +E +   + YTSGTT
Sbjct: 130 HRFVLGHDEELFAPEGAEPKAWE---------------------PDENATACINYTSGTT 168

Query: 200 GLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCL 259
             PKGV   HR  ++NA+   L   +    V L TLPMFHA  WG  +A   +G  +V L
Sbjct: 169 ARPKGVQITHRNIWVNAVTFALHVGLTDRDVILHTLPMFHANGWGMPFAATGLGIKHVVL 228

Query: 260 DKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMK--RNNLKFSNRVHMLVAGAAPAPAT 317
            K+D   I R V  E VT MCAAP V  ++ +  +     +   +RV ++VAGA P   T
Sbjct: 229 RKIDGTEILRRVRDEGVTFMCAAPAVVASVLEAAQSWEGEIPGRDRVRIIVAGAPPPTKT 288

Query: 318 LKAMQ-EIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDV 376
           +  ++ E+G     +YGLTET    +I   R EWD LP+EE+A    R G P +      
Sbjct: 289 VARVETELGWEFIQIYGLTETSPLLTINRSRAEWDDLPVEERAGKLIRAGQPAI------ 342

Query: 377 FDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIE 436
               G  +  D +  GEV+ R + +  GY++ PE+TA +   GWFH+GD  V+  DGY+ 
Sbjct: 343 ----GVTLATDPE--GEVLARSNVILEGYWQQPEETARALDGGWFHTGDGGVIGEDGYLT 396

Query: 437 IVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKL 496
           I DR KD+I TGGE VSSI VE  L   P V  VAV G P EKWGE + A + L  G + 
Sbjct: 397 ISDRKKDVIITGGENVSSIEVEDALFSHPAVAEVAVIGVPSEKWGETIKALVVLAPGAQA 456

Query: 497 TEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537
           TE ++I +CKERLA ++ P  VEF   +  TATGK+QK+ LR
Sbjct: 457 TEADLIGWCKERLAGYKAPTSVEFRDELARTATGKLQKFKLR 498


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: 679
Number of extensions: 32
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: 549
Length of database: 510
Length adjustment: 35
Effective length of query: 514
Effective length of database: 475
Effective search space:   244150
Effective search space used:   244150
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