GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pseudomonas fluorescens GW456-L13

Align Sorbitol dehydrogenase; SDH; (R,R)-butanediol dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.4; EC 1.1.1.14; EC 1.1.1.56; EC 1.1.1.9 (characterized)
to candidate PfGW456L13_3657 Threonine dehydrogenase and related Zn-dependent dehydrogenases

Query= SwissProt::Q00796
         (357 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3657
          Length = 339

 Score =  172 bits (436), Expect = 1e-47
 Identities = 108/335 (32%), Positives = 173/335 (51%), Gaps = 30/335 (8%)

Query: 14  VHGPGDLRLENYPIPEPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMVLGHEAS 73
           +HGP DLR++  P+P PG  +VL+ + + G+CGSD+ ++E G I       PM LGHE S
Sbjct: 10  LHGPRDLRVDEVPLPSPGETDVLVEVAACGVCGSDLGFYESGGIRRD--GAPMPLGHEFS 67

Query: 74  GTVEKVGSSVKHLKPGDRVAIEPGAPRENDEFCKMGRYNLSPSIFFCATPPDDGNLCRFY 133
           G + +VG++V H +PG RV + P A   N     +G               D+G L    
Sbjct: 68  GVIREVGTAVVHYRPGMRVVVNPMA---NGAMIGVGS--------------DEGALANLV 110

Query: 134 K----HNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGAGPIGMVTL 189
           +    ++    ++LP N+  E  AL+EPL+V +HA  R  VT G  VLV GAG IG+  +
Sbjct: 111 RVRNVNSGPILHQLPANLPLEVAALVEPLAVALHAVNRSRVTAGESVLVLGAGAIGLGIV 170

Query: 190 LVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKESP-QEIAR---KVEGQLGCK-- 243
              KA G +Q+ V DLSA RL  A  +GA+L L  +++    E+AR    V   LG +  
Sbjct: 171 ACLKARGISQIAVADLSAGRLEIAAGLGANLTLDPTRDDLWSELARAHGSVPTFLGTQAP 230

Query: 244 -PEVTIECTGAEASIQAGIYATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKGVFRYCN 302
             +V  EC+G    +   I   R    + +  +  +          ++E+++ G   Y  
Sbjct: 231 ATQVIFECSGVSGVLHEAIARARDAARITVASVYKQPQAFDFSILQVKELELIGTLCYPT 290

Query: 303 TWPVAISMLASKSVNVKPLVTHRFPLEKALEAFET 337
            +  A+ +LAS + + + +++HRF L+   +A++T
Sbjct: 291 EFAQALELLASGAFDPESMISHRFSLDDVAQAYKT 325


Lambda     K      H
   0.319    0.137    0.415 

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: 286
Number of extensions: 12
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: 357
Length of database: 339
Length adjustment: 29
Effective length of query: 328
Effective length of database: 310
Effective search space:   101680
Effective search space used:   101680
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: 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