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_091295014.1 BLV57_RS31585 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_900107045.1:WP_091295014.1
          Length = 565

 Score =  360 bits (923), Expect = e-103
 Identities = 221/522 (42%), Positives = 302/522 (57%), Gaps = 25/522 (4%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FNW  D F+ I   +  ++ AL  R ++      ++Y ELS  S+RV + LR+ G+ +G+
Sbjct: 36  FNWALDWFDAI--AQGNTRDAL--RIVDGASVTSVTYEELSRRSSRVANWLREQGVDRGN 91

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V LM       W   LA +K G V++P+ T +  A++    +D      +S  +  + +
Sbjct: 92  RVLLMLDNQAAVWETLLAAMKLGAVVIPTYTTIGPADL----ADRLERGAVSHVITTAAL 147

Query: 158 EEALGSLKVEKFLIDGKRETWNSLEDESSNAEPE-----DTRGEDVIINYFTSGTTGMPK 212
             A     + K ++    + W    D +++A PE      T  +  +  YFTSGTT  PK
Sbjct: 148 TGAFAQADLTKIVVGPPVDGWLDYAD-AAHASPEFVPDGPTPADQELFLYFTSGTTSKPK 206

Query: 213 RVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGI-NY 271
              H   SYPVG ++     GV+  D+HLN+SA GWAK AWSSFF P    ATV+ + N 
Sbjct: 207 LAQHNHTSYPVGHLSGMYWNGVQPGDVHLNISAPGWAKHAWSSFFVPFNAEATVLSVANP 266

Query: 272 EGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIK 331
            G       L  +   G T+FCAPPT WR  I  DL Q+   RLR   S GEPLNPEVI+
Sbjct: 267 TGSAQV--VLDALVEHGATTFCAPPTVWRLLIQQDLRQWPV-RLREAGSVGEPLNPEVIE 323

Query: 332 IWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEIT-KPY 390
             +  + +T+RD +GQTETTA +GN   L V+PGSMGKP P Y+I L+D     IT +P 
Sbjct: 324 HVRQAWGITVRDAFGQTETTAQIGNTAGLPVRPGSMGKPLPGYEIVLIDP----ITGQPA 379

Query: 391 EVGHITVKLNPRPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVI 449
           + G I VKL+PRP+G+  GY  + +KN E+F  GYY+TGD A  D +GY  +VGR DDV 
Sbjct: 380 DEGEICVKLDPRPVGVMSGYLGNPEKNAETFGGGYYHTGDIASRDADGYLTYVGRADDVF 439

Query: 450 KTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIR 509
           K+ DYRV PFE+ES LLEH  VAEAAVV  PD V   + KA++ L  G  PS+  A  I 
Sbjct: 440 KSYDYRVSPFELESVLLEHDEVAEAAVVPSPDVVGLVVPKAFVTLAAGAEPSESTARSIL 499

Query: 510 EKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEK 551
             ++  L+P++  R +EF   LPKT SGKIRR ELRK+E+ +
Sbjct: 500 AHVQDQLAPHQWIRRLEF-GPLPKTTSGKIRRAELRKQEDAR 540


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: 771
Number of extensions: 39
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: 564
Length of database: 565
Length adjustment: 36
Effective length of query: 528
Effective length of database: 529
Effective search space:   279312
Effective search space used:   279312
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