GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas simiae WCS417

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF2136 PS417_10895 AMP-dependent synthetase

Query= BRENDA::A4YDT1
         (564 letters)



>FitnessBrowser__WCS417:GFF2136
          Length = 566

 Score =  373 bits (957), Expect = e-107
 Identities = 223/544 (40%), Positives = 300/544 (55%), Gaps = 36/544 (6%)

Query: 35  LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94
           L  FNW  D F+ +     G+    +W     G E + S+ +L+  SN+V + LR  G+ 
Sbjct: 31  LGEFNWALDYFDAM---AEGNPADALWIVEEDGSEQRYSFQQLAARSNQVANHLRALGVN 87

Query: 95  KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154
           +GD V LM       W   LA  K G V++P+   L   +++ R              R 
Sbjct: 88  RGDRVLLMLGNDVALWDTMLAAFKLGAVVIPATALLNPDDLRDRIE------------RG 135

Query: 155 SVMEEALGSLKVEKFL----------IDGKRETWNSLEDESSNAEPEDTRGE----DVII 200
            V    +G   V KF           +      W +        E  + +G     D ++
Sbjct: 136 QVRHVVVGEAHVHKFAGLAQGCSRICVGSAPAGWVAHNAAFEYPEQFEAQGRTLATDPML 195

Query: 201 NYFTSGTTGMPKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPL 260
            YFTSGTT  PK V+H+  SYPVG ++T   +G++  DLHLN+S+ GWAK AWS  F+P 
Sbjct: 196 LYFTSGTTSKPKMVLHSHQSYPVGHLSTMYWIGLQPGDLHLNISSPGWAKHAWSCLFAPW 255

Query: 261 LVGATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFE-RLRSVV 319
             GA +  I+   +      L  +E  GVTS CAPPT WR  I  DL  +R    LR +V
Sbjct: 256 NAGACIF-IHNVARFSAPALLSALERYGVTSLCAPPTVWRMLIQEDLASYRPRLSLRELV 314

Query: 320 SAGEPLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLL 379
            AGEPLNPE+I+  +  + L +RD +GQ+ETTA+VGN P   +KPGSMG+P P Y + LL
Sbjct: 315 GAGEPLNPEIIEQIQQAWGLPLRDGFGQSETTALVGNTPGQLLKPGSMGRPLPGYQVALL 374

Query: 380 DDEGKEITKPYEVGHITVKLNPRPIGLFLGYSDE-KKNMESFREGYYYTGDKAYFDEEGY 438
           D +G     P   G + + L+ RP+GL L Y D  +K  E  R+GYY TGD A  D +GY
Sbjct: 375 DPDGI----PGNEGEVALPLDVRPLGLMLCYEDSPEKTAEVMRDGYYRTGDTAQIDADGY 430

Query: 439 FYFVGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGY 498
             FVGR DDV K SDYR+ PFE+ESAL+EHPAV E AVV  PD +R  + KA+++L    
Sbjct: 431 ITFVGRADDVFKASDYRISPFELESALIEHPAVMEVAVVPSPDPLRLAVPKAFLILAHDE 490

Query: 499 MPSKELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVG 558
             S  LA+ I    +  L+PYK  R IEFV ELPKTISGKIRRVELR+ E  +R+    G
Sbjct: 491 PGSAALAQHILAFAREHLAPYKRVRRIEFVTELPKTISGKIRRVELRQMEVLRRQGDTRG 550

Query: 559 QNEY 562
           ++E+
Sbjct: 551 EHEH 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: 747
Number of extensions: 35
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: 566
Length adjustment: 36
Effective length of query: 528
Effective length of database: 530
Effective search space:   279840
Effective search space used:   279840
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 17 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