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_110207305.1 DNK54_RS12540 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_003194585.1:WP_110207305.1
          Length = 577

 Score =  355 bits (911), Expect = e-102
 Identities = 225/538 (41%), Positives = 303/538 (56%), Gaps = 19/538 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+V D F+      RG+    +      G  A  S+ EL   S +V   L   G++ GD
Sbjct: 41  FNFVHDWFD---AYARGNDRPGLVIVEEDGRRASYSFGELVTRSEQVAQHLSALGVRAGD 97

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157
            V +M       W   LA+I+ G V++P+ T +  AE+  R       A++ ++  A+  
Sbjct: 98  SVVVMLGNQVELWESMLALIRLGAVIMPTTTAVGPAELVDRLDRGAARAVVCNAADAAKF 157

Query: 158 EEALGS-LKVEKFLIDGKRETWNSLEDESSNA----EPEDTRGEDVIINYFTSGTTGMPK 212
           +E  G+ L+V          ++ +  D  + A    E      +D ++ YFTSGTT  PK
Sbjct: 158 DEVPGAYLRVAVGEAPTGWASYAAAYDRDAGAVATLEHPGNGSDDRLLLYFTSGTTSRPK 217

Query: 213 RVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYE 272
            V HT  SYP+G ++T   +G++  D+HLN+S+ GWAK AWS+FF+P L  ATV   NY 
Sbjct: 218 LVEHTHTSYPIGHLSTMYWLGLQPGDVHLNISSPGWAKHAWSNFFAPWLAEATVFVYNY- 276

Query: 273 GKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKI 332
            + D    LG++   GVT+FCAPPT WR  I  DL       LR  ++AGEPLNPEVI  
Sbjct: 277 ARFDAMALLGQIRTEGVTTFCAPPTVWRMLINADLSGGPGV-LREAIAAGEPLNPEVISQ 335

Query: 333 WKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEV 392
            +  + LTIRD +GQTE TA + N P   VK GSMG+P P   I L+D     + +    
Sbjct: 336 VERHWGLTIRDGFGQTEMTAAIANAPGQPVKAGSMGRPLPGVPIVLVDPVEGSVVEGVGE 395

Query: 393 GHITVKLNPR----PIGLFLGYS-DEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDD 447
           G I + L+ R    P+ L  GY  DE+KN E+   G+++TGD A  DEEG   +VGR DD
Sbjct: 396 GEICLDLSVRDGAGPLTLMTGYQGDEEKNAEAMAGGFFHTGDVASRDEEGQITYVGRTDD 455

Query: 448 VIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEE 507
           V K SDY+V PFE+ES LLEHPAVAEAAVV  PD VR  + KAY+ L  G+ P+ E A+ 
Sbjct: 456 VFKASDYKVSPFELESVLLEHPAVAEAAVVPAPDPVRLAVPKAYVALVPGHEPTAETAKS 515

Query: 508 IREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEE---KRKKGEVGQNEY 562
           I    +  L+PY   R +EF  ELPKTISGKIRRVELR+RE E    R  GE    ++
Sbjct: 516 ILHYAREHLAPYLRVRRLEFY-ELPKTISGKIRRVELRQRENEVEGSRLDGEYRDEDF 572


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: 748
Number of extensions: 30
Number of successful extensions: 6
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: 577
Length adjustment: 36
Effective length of query: 528
Effective length of database: 541
Effective search space:   285648
Effective search space used:   285648
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