GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Lentibacillus jeotgali Grbi

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_010529673.1 ON01_RS03745 acyl--CoA ligase

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_000224785.1:WP_010529673.1
          Length = 526

 Score =  339 bits (870), Expect = 1e-97
 Identities = 198/504 (39%), Positives = 295/504 (58%), Gaps = 14/504 (2%)

Query: 56  KTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWAVFLA 115
           + A++W     GE  +++Y +L    N++ +  ++ GL+KGD V +M       +  +LA
Sbjct: 28  RNAVVWCS-EKGESKEITYEQLMKNVNKIGNAFKEKGLEKGDRVLIMIPRLIEAYETYLA 86

Query: 116 VIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLIDGKR 175
            +K G +++P +  L   +++YR S  + SAI+S         +     ++  F +    
Sbjct: 87  ALKSGIIVIPGSEMLKTKDLQYRISHGEVSAIVSYYPYVGQFTDVKEFEQLTLFSVGNSV 146

Query: 176 ETWNSLEDESSNAEPE----DTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSITTA-- 229
           + W++++    NA  +    DT  +DV    +TSGTTG PK V+HT   +    + TA  
Sbjct: 147 DGWHNMDKLKENASDKLDMADTTKDDVAFFSYTSGTTGNPKAVVHTH-GWGYAHLNTAPE 205

Query: 230 SIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVENLGV 289
           + + + E D     +  GW K+ WS F S L  GAT  G  Y GK D + YLG +++  +
Sbjct: 206 NWLCINEGDKVWATAGPGWQKWIWSPFLSVLGSGAT--GFVYLGKFDPKTYLGLLQDEDI 263

Query: 290 TSFCAPPTAWRQFITLD-LDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQT 348
              C  PT +R    +D LD ++   L S VSAGEPLN EVI  ++  FN+T+RD YGQT
Sbjct: 264 NVLCCTPTEYRLMAKVDNLDDYQLPALHSAVSAGEPLNREVIDTFRKYFNVTVRDGYGQT 323

Query: 349 ETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPIGLFL 408
           E T ++G     KVKPGSMGKP P  ++ +++++G+ +    ++G I VKL+  P     
Sbjct: 324 ENTLLLGFMKDTKVKPGSMGKPTPGNEVEIINEDGQPVPAN-KIGDIAVKLDS-PALFRE 381

Query: 409 GYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALLEH 468
            Y D ++   S R  YY TGD+A  DE+GYF+F GR DD+I +S Y +GPFEVE AL++H
Sbjct: 382 YYKDAERTRMSQRGEYYVTGDQASKDEDGYFWFEGRSDDIIISSGYTIGPFEVEDALVKH 441

Query: 469 PAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMP-SKELAEEIREKMKTLLSPYKVPRIIEF 527
           P V E AVV  PD VR  +VKA+IVL++G  P   +L  ++++ +K L +PYK PR IEF
Sbjct: 442 PFVQECAVVASPDEVRGNVVKAFIVLQQGVNPDDPDLVRDLQKHVKELTAPYKYPRKIEF 501

Query: 528 VDELPKTISGKIRRVELRKREEEK 551
           +DELPKT SGKIRRVELR+ E+ K
Sbjct: 502 IDELPKTTSGKIRRVELRQNEKVK 525


Lambda     K      H
   0.318    0.137    0.402 

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: 785
Number of extensions: 50
Number of successful extensions: 7
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: 564
Length of database: 526
Length adjustment: 35
Effective length of query: 529
Effective length of database: 491
Effective search space:   259739
Effective search space used:   259739
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.

Links

Downloads

Related tools

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