GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Microvirga lotononidis WSM3557

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_009764221.1 MICLODRAFT_RS22930 benzoate-CoA ligase family protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_000262405.1:WP_009764221.1
          Length = 557

 Score =  234 bits (597), Expect = 7e-66
 Identities = 163/503 (32%), Positives = 255/503 (50%), Gaps = 31/503 (6%)

Query: 61  WRDINTGEEA-------KLSYHELSLMSNRVLSTL-RKHGLKKGDVVYLMTKVHPMHWAV 112
           W D   G+E         L+Y  L    NR+ + L  + G   G+ V L +  +PM  A 
Sbjct: 47  WVDEGRGDEPCIISPTETLTYRTLQERVNRICNVLVHRLGFVPGNRVLLRSANNPMMVAA 106

Query: 113 FLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLID 172
           +LAV+K G V+V +   L   E+ Y  +  + +  + D   A  ME A       + ++ 
Sbjct: 107 YLAVLKAGGVVVATMPLLRAKEIAYPLNKAQITIALCDHRLADEMERARAMAPGLQHVVY 166

Query: 173 GKRETWNSLEDESSNAEPE----DTRGEDVIINYFTSGTTGMPKRVIH-----TAVSYPV 223
                 +SLE   + A PE    DT  +DV +  FTSGTTG PK  +H      A+    
Sbjct: 167 WGSGQPDSLEAMIAEASPEFAAVDTAADDVCLIGFTSGTTGEPKGTMHFHQDMLAICDGY 226

Query: 224 GSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGE 283
           G     +++     D  +      +          P+ VGA+ V +   G  D    L  
Sbjct: 227 GR----NVLRPEPDDRFIGSPPLAFTFGLGGIVLFPMRVGASTVLLEKAGPDDL---LPA 279

Query: 284 VENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRD 343
           ++    T     PTA+R  ++  L+ +    LR  VSAGEPL     + WK    + + D
Sbjct: 280 IQQYKATICFTAPTAYRAMLS-KLEGYDISSLRKCVSAGEPLPKGTFEAWKAATKIRLMD 338

Query: 344 FYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRP 403
             G TE   +       +++PG+ GKP P Y+ +++DDEG+++  P  +G + V+    P
Sbjct: 339 GIGATEMLHIFIAATEDEIRPGATGKPVPGYEAKVVDDEGRDLP-PGSIGRLAVR---GP 394

Query: 404 IGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVES 463
            G    Y  +++  +  ++G+  TGD    DE+GYF++  R DD+I ++ Y +   EVE+
Sbjct: 395 TGC--RYLADERQRKYVQDGWNITGDTYLMDEDGYFWYQARSDDMIISAGYNIAGPEVEA 452

Query: 464 ALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPR 523
           ALL HPAVAE  VVG PD  R  +VKAY+VL+ G++P  EL + +++ +K  ++PYK PR
Sbjct: 453 ALLTHPAVAECGVVGAPDDGRGTVVKAYVVLRSGHVPGPELTKVLQDHVKAEIAPYKYPR 512

Query: 524 IIEFVDELPKTISGKIRRVELRK 546
           +IEFVD LP+T +GK++R ELR+
Sbjct: 513 LIEFVDALPRTQTGKLQRFELRR 535


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: 669
Number of extensions: 31
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 564
Length of database: 557
Length adjustment: 36
Effective length of query: 528
Effective length of database: 521
Effective search space:   275088
Effective search space used:   275088
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: 53 (25.0 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