GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Ochrobactrum rhizosphaerae PR17

Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate WP_094578795.1 CEV32_RS19735 alcohol dehydrogenase AdhP

Query= BRENDA::Q97YM2
         (349 letters)



>NCBI__GCF_002252475.1:WP_094578795.1
          Length = 344

 Score =  137 bits (346), Expect = 3e-37
 Identities = 104/345 (30%), Positives = 168/345 (48%), Gaps = 17/345 (4%)

Query: 10  KAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILG 69
           KAA++++F +PL+I++V IP+P   ++ + I  +GVC TDL   +G +       P I G
Sbjct: 6   KAAVVREFGKPLTIDEVPIPQPGDGQIQVAIQASGVCHTDLHAAEG-DWPVKPNPPFIPG 64

Query: 70  HENAGTIVEVGELAK-VKKGDNVVV---YATWGDLTCRYCREGKFNICKNQIIPGQTTNG 125
           HE  G +  VG+  K VK+GD V +   Y   G   C +C  G   +C+ Q+  G + NG
Sbjct: 65  HEGVGFVSAVGKGVKHVKEGDRVGIPWLYTACGH--CVHCLGGWETLCEEQLNTGYSVNG 122

Query: 126 GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIG 185
           GF++Y++   +       ++   E AP+  AG T    + + L          V+++GIG
Sbjct: 123 GFADYVVADPNFVGHLPKNIEFNEIAPILCAGVT----VYKGLKVTDTKPGDWVVISGIG 178

Query: 186 GLAVYTIQILKALMKNITIVGISRSKKHRDFALELGADYVSEMK---DAESLINKLTDGL 242
           GL    +Q  KA+  N+  V I    K  D A  LGA      K   D  + I K TDG 
Sbjct: 179 GLGHMAVQYAKAMGLNVAAVDI--DDKKLDLARRLGATVTVNAKTHNDPAAYIKKETDGG 236

Query: 243 GASIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSL 302
              + +  V  +     +G + A+ G I L G+      L  F+  +    + GS  G+ 
Sbjct: 237 AQGVLVTAVSPKAFEQAIG-MAARGGTIALNGLPAGDFPLSIFNMVLNGVTVRGSIVGTR 295

Query: 303 NDLEDVVRLSESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVI 347
            DL++ +  +  GK+K  I    +D+IN  F  +  G+++GR V+
Sbjct: 296 LDLQESIDFAADGKVKATIRTDKIDNINAIFDEMRAGQIEGRVVM 340


Lambda     K      H
   0.317    0.136    0.389 

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: 292
Number of extensions: 17
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: 349
Length of database: 344
Length adjustment: 29
Effective length of query: 320
Effective length of database: 315
Effective search space:   100800
Effective search space used:   100800
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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