GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas simiae WCS417

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF5420 PS417_27745 aldehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__WCS417:GFF5420
          Length = 497

 Score =  194 bits (493), Expect = 6e-54
 Identities = 145/466 (31%), Positives = 230/466 (49%), Gaps = 12/466 (2%)

Query: 4   WINGDWITGQGASRVKR-NPVSGEVLWQGNDADAAQVEQACRAARAAFPR--WARLSFAE 60
           +ING++         +  +PV G +L      DAA  ++A   ARA F    W+RL+ A+
Sbjct: 23  YINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAK 82

Query: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAAT-EVTAMINKIAISIKAYHVRTGEQ 119
           R + + RFAALL++N  EL  +   + GKP  ++   +V    N ++ S +A      E 
Sbjct: 83  RKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALSWSGEAIDKIYDEV 142

Query: 120 RSEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEA 179
            +   D    +   P GV+    P+NFP  +    + PAL  GN++I KPSE +P +   
Sbjct: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIR 202

Query: 180 VMRLWQQAGLPPGVLNLVQG-GRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEK 238
           +  L  +AG+P GV N++ G G   G AL+   D+D L+FTGS     QL  +      K
Sbjct: 203 IAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMK 262

Query: 239 ILALEMGGNNP-LIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLAR 297
            + LE GG +P ++  +  D+ AA      +     G+ CT   RLL++   + D FL  
Sbjct: 263 RVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIK-DKFLPL 321

Query: 298 LVAVSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPR--LLQAGT 355
           ++   +   PGN  D P   +G L+  Q    V++  +   A G + +   +  L + G 
Sbjct: 322 VIEALKGWKPGNPLD-PATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLEETGG 380

Query: 356 SLLTPGIIE-MTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREK 414
           + + P I + +T    +  EE+FGP+L V  +D+ +EA+ +AN+T +GL+  + + +  K
Sbjct: 381 TYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISK 440

Query: 415 FDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460
                   RAG V W     G   TAPFGG   SGN R  + +A D
Sbjct: 441 AHLTAKALRAGSV-WVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFD 485


Lambda     K      H
   0.318    0.134    0.412 

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: 642
Number of extensions: 33
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: 492
Length of database: 497
Length adjustment: 34
Effective length of query: 458
Effective length of database: 463
Effective search space:   212054
Effective search space used:   212054
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: 52 (24.6 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