GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pseudomonas putida KT2440

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate PP_0552 PP_0552 2,3-butanediol dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__Putida:PP_0552
          Length = 362

 Score =  197 bits (502), Expect = 3e-55
 Identities = 121/361 (33%), Positives = 187/361 (51%), Gaps = 15/361 (4%)

Query: 1   MTHTVPQNMKAAVMHNTREIKIETLPVP-DINHDEVLIKVMAVGICGSDLHYYTNGRIGN 59
           ++HT   +M+AAV H   +I++E +P+P D     V IKV   GICGSDLH Y  G +  
Sbjct: 4   LSHT---HMRAAVWHGRHDIRVEQVPLPADPAPGWVQIKVDWCGICGSDLHEYVAGPVFI 60

Query: 60  YV--------VEKPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRY 111
            V        ++   ILGHE  G IA +G  V+ + VGD VA +    CG C  C  G Y
Sbjct: 61  PVEAPHPLTGIQGQCILGHEFCGHIAKLGEGVEGYAVGDPVAADACQHCGTCYYCTHGLY 120

Query: 112 NLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQ 171
           N+C  + F      +GAF + + +  + ++ +P     E  ALIEP +VG+HA  +    
Sbjct: 121 NICERLAFTGLMN-NGAFAELVNVPANLLYRLPQGFPAEAGALIEPLAVGMHAVKKAGSL 179

Query: 172 PGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALE 231
            G T+ ++G G +GL  +  AKA GA  +I  ++   R   AK+ GA  +++  + DAL 
Sbjct: 180 LGQTVVVVGAGTIGLCTIMCAKAAGAAQVIALEMSSARKAKAKEAGANVVLDPSQCDALA 239

Query: 232 EIKTITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEI 291
           EI+ +T   G DV++E  GN    + A+ ++R+ GK  +VG+  +     N   +   E 
Sbjct: 240 EIRALTAGLGADVSFECIGNKHTAKLAIDTIRKAGKCVLVGI-FEEPSEFNFFELVSTEK 298

Query: 292 DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQD-AMERALQFKNECLKVMVY 350
            + G   Y   +   I F+A G +D + LVT +  LEQ  +   E  +  K E +K++V 
Sbjct: 299 QVLGALAYNGEFADVIAFIADGRLDIRPLVTGRIGLEQIVELGFEELVNNKEENVKIIVS 358

Query: 351 P 351
           P
Sbjct: 359 P 359


Lambda     K      H
   0.320    0.137    0.401 

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: 323
Number of extensions: 20
Number of successful extensions: 5
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: 353
Length of database: 362
Length adjustment: 29
Effective length of query: 324
Effective length of database: 333
Effective search space:   107892
Effective search space used:   107892
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 (21.8 bits)
S2: 49 (23.5 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