GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Dechlorosoma suillum PS

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Dsui_2187 Dsui_2187 acyl-CoA synthetase/AMP-acid ligase

Query= BRENDA::A4YDT1
         (564 letters)



>FitnessBrowser__PS:Dsui_2187
          Length = 565

 Score =  424 bits (1090), Expect = e-123
 Identities = 233/534 (43%), Positives = 328/534 (61%), Gaps = 17/534 (3%)

Query: 35  LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94
           L  FNW  D F+   V  +G+    +W     G E K+S+ ++S  SN+V + L+  G+K
Sbjct: 33  LTEFNWALDHFD---VMAKGNDKPALWIVEEDGTEHKISFAQMSARSNQVANWLKAQGVK 89

Query: 95  KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154
           +GD + +M       W   L  IK G V++P+ T LT  +++ R    +   +I  +   
Sbjct: 90  RGDRILMMLGNEVPLWETMLGCIKLGAVLIPATTLLTPEDLRDRLDRGQVKHVIIGAAHT 149

Query: 155 SVMEEALGSLKVEKFLIDGKRETWNSLEDE---SSNAEPED-TRGEDVIINYFTSGTTGM 210
               +  G     +  + G+   W + +D    S+   P+  T+  D ++ YFTSGTT  
Sbjct: 150 DKFTDLAGDYT--RICVGGEPAGWKAFKDSHTASAEYTPDAATKVSDPLLLYFTSGTTSK 207

Query: 211 PKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGIN 270
           PK V+HT  SYPVG ++T   +G++  D+HLN+S+ GWAK AWS FF+P   GA +   N
Sbjct: 208 PKLVLHTHQSYPVGHLSTMYWIGLQPGDIHLNISSPGWAKHAWSCFFAPWNAGACIFLYN 267

Query: 271 YEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFE-RLRSVVSAGEPLNPEV 329
           Y  +   +  L  +E   VT+ CAPPT WR  I  DL  ++   ++R ++ AGEPLNPE+
Sbjct: 268 YS-RFSAKSMLNVLEKYQVTTMCAPPTVWRMMIQEDLAAYKGRLKIRELIGAGEPLNPEI 326

Query: 330 IKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKP 389
           I+  ++ +N+TIRD +GQTETTA +GN P   +KPGSMG+P P Y + L+D EG E  + 
Sbjct: 327 IEQLQNAWNITIRDGFGQTETTAEIGNTPGQPLKPGSMGRPLPGYQVVLVDSEGNEAAE- 385

Query: 390 YEVGHITVKLNPRPIGLFLGYS-DEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDV 448
              G I++KLNPRP+GL +GYS D +K  E  R+G Y+TGD A  DE+GY  +VGR DDV
Sbjct: 386 ---GEISLKLNPRPLGLMVGYSGDAEKTAEVMRDGVYHTGDVATKDEDGYITYVGRADDV 442

Query: 449 IKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEI 508
            K SDYR+ PFE+ES L+EHPAVAEAAVV  PD VR  + KAY++L+ G  PSKELA++I
Sbjct: 443 FKASDYRISPFELESVLIEHPAVAEAAVVPSPDPVRLAVPKAYVILRNGEKPSKELAKDI 502

Query: 509 REKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVGQNEY 562
              ++  L+PYK  R +EF D LPKTISGKIRRVELR  E ++R   E G+ E+
Sbjct: 503 FAFLRANLAPYKRIRRLEFSD-LPKTISGKIRRVELRANEAKRRNANEKGEWEF 555


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: 791
Number of extensions: 39
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: 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 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