GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Amycolatopsis xylanica CPCC 202699

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_091286304.1 BLV57_RS03085 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_900107045.1:WP_091286304.1
          Length = 557

 Score =  367 bits (943), Expect = e-106
 Identities = 215/533 (40%), Positives = 304/533 (57%), Gaps = 17/533 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FNW  D F++I      ++   +W     G E + ++ E++  S++V + LR  G+++GD
Sbjct: 31  FNWALDWFDEIARDPANAERYALWIVEEDGSENRWTFPEMARRSDQVANWLRSLGVRRGD 90

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            + LM       W   LA IK G V++P++T L  A++  R        ++  +   +  
Sbjct: 91  RLILMLGNQGELWETILASIKLGAVIIPASTLLGPADLTDRVERGAAKHVVIRAEDTAKF 150

Query: 158 EEALGSLKVEKFLIDGKRETWNSLEDESSNAEPE-----DTRGEDVIINYFTSGTTGMPK 212
               G     +  +    + W S  D S +A  E      T+ +D ++ YFTSGTT  PK
Sbjct: 151 ATVAGDYT--RIAVGDAVDGWVSYSD-SQDAPAEFRPDGPTKADDALLLYFTSGTTAKPK 207

Query: 213 RVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYE 272
            V HT VSYPVG ++T   +G+   D+HLN+S+ GWAK AWS+ F+P    ATV   NY 
Sbjct: 208 LVRHTQVSYPVGHLSTMYWIGLEPGDVHLNISSPGWAKHAWSNVFAPWNAEATVFLYNYT 267

Query: 273 GKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKI 332
            + D    + +++  G+TSFCAPPT WR  I  DL   +    R VV AGEPLNPEVI  
Sbjct: 268 -RFDAAALMAQMDRCGITSFCAPPTVWRMLIQADLTALKTPP-RKVVGAGEPLNPEVIDQ 325

Query: 333 WKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEV 392
            +  + +TIRD +GQTE++  + N P   V PGSMG+P P + + L+D    E+      
Sbjct: 326 VRKAWGVTIRDGFGQTESSVQIANTPGQDVVPGSMGRPLPGFKVALVDPVSGEVASE--- 382

Query: 393 GHITVKLNPRPIGLFLGYSDEKKNMES-FREGYYYTGDKAYFDEEGYFYFVGRGDDVIKT 451
           G I + L+ RP+GL  GY+D+ +  E+ F  GYY+TGD    D  GY  +VGR DDV K 
Sbjct: 383 GEICLDLSARPVGLMTGYADDDERTEAAFAGGYYHTGDVGSVDANGYITYVGRTDDVFKA 442

Query: 452 SDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREK 511
           SDYR+ PFE+ES LLEH AVAEAAVV   D +R  + KA++VL  G+ P+ E A+ I   
Sbjct: 443 SDYRISPFELESVLLEHDAVAEAAVVPAADPIRLAVPKAFVVLAAGHTPTAETAQSILAF 502

Query: 512 MKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKR--EEEKRKKGEVGQNEY 562
            +  L+PYK  R +EF  ELPKTISGKIRRVELR R  + + R  GE  + ++
Sbjct: 503 CREHLAPYKRIRRLEFA-ELPKTISGKIRRVELRNRAGDADLRPTGEFREEDF 554


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: 758
Number of extensions: 35
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: 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