GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Echinicola vietnamensis KMM 6221, DSM 17526

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases

Query= reanno::WCS417:GFF5420
         (497 letters)



>FitnessBrowser__Cola:Echvi_3822
          Length = 453

 Score =  230 bits (587), Expect = 7e-65
 Identities = 141/457 (30%), Positives = 236/457 (51%), Gaps = 9/457 (1%)

Query: 40  ISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAE 99
           I+P  G LL           + A++  +  + S  W  L  ++R   M +   +L+ N +
Sbjct: 4   INPYTGELLEEFTDHTEQQVEAAIQKGQEAYLS--WRELPISQRADLMKKAGQVLRDNTD 61

Query: 100 ELALLETLDMGKPISDSLNIDVPGAANALSWSGE-AIDKIYDEVAATPHDQLGLVTREPV 158
           +   + +L+MGK I++S + +V   A    +  E A + + D   A P  +   V   P+
Sbjct: 62  KYGKIISLEMGKVITESKS-EVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPL 120

Query: 159 GVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFN 218
           G+V A++PWNFP         P L+ GN  +LK +   P  A+ I  +  +AG P+GVF 
Sbjct: 121 GIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVFQ 180

Query: 219 VLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFA 278
            L      V N +A H DV     TGS K  +++  ++GE  +K+  LE GG  P IV  
Sbjct: 181 SLLIGSDKVANIIA-HPDVKAATLTGSEKAGQKIAAQAGEQ-IKKTVLELGGSDPFIVLK 238

Query: 279 DAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPA 338
           DA D++ AA++AA     N G+ C A  R ++E+ + D+F+     A++ + PG+PLD  
Sbjct: 239 DA-DVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEK 297

Query: 339 TNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIA 398
                +        +   +EA    GA+++  G  T  E G  +++P I   +T  M   
Sbjct: 298 AGYACMARPDLAMELYEQVEASIQKGAEVILEG--TKPEKGKAFIKPYILGKLTPDMPAY 355

Query: 399 KEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQY 458
           +EE+FGPV SV   +  +EA+AIAND+ +GL A++WT D  KA + ++ + +G+V++N  
Sbjct: 356 REELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSM 415

Query: 459 DGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWI 495
              +   PFGG K+SG GR+ + +   ++  +K  ++
Sbjct: 416 VASNPYLPFGGIKKSGYGRELAENGIKEFMNIKTVYL 452


Lambda     K      H
   0.316    0.132    0.386 

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: 478
Number of extensions: 18
Number of successful extensions: 4
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: 497
Length of database: 453
Length adjustment: 33
Effective length of query: 464
Effective length of database: 420
Effective search space:   194880
Effective search space used:   194880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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