GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Catellicoccus marimammalium M35/04/3

Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_040388552.1 C683_RS01375 SDR family oxidoreductase

Query= curated2:P37079
         (267 letters)



>NCBI__GCF_000313915.1:WP_040388552.1
          Length = 273

 Score =  122 bits (306), Expect = 8e-33
 Identities = 89/273 (32%), Positives = 127/273 (46%), Gaps = 28/273 (10%)

Query: 8   KDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNYH-------FWSTDI 60
           KD V+I+TG A GIG A       +GA + + D          +          F   D+
Sbjct: 12  KDKVMIITGAAGGIGKACAIRAAKEGAKLVLGDQKEEMSQETLEEIQKITPDVDFLVGDL 71

Query: 61  SSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQ 120
                 Q  +   I+++ RID LVNNAG+           PA  +E++E  F  +++ N 
Sbjct: 72  CEEKNCQALVQTAIEKYGRIDILVNNAGIT--------GIPAPVHEMSEEMFRHVLDSNI 123

Query: 121 KGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGK 180
              F+ S+A    M++Q  G I+NVSS +GL G  G S Y  +K  LN  TR+ + +   
Sbjct: 124 MIAFYCSKATLPYMMEQHNGSIINVSSVAGLTGFPGHSAYVTSKHGLNGLTRNMALDYAS 183

Query: 181 YGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREG--------YTKNAIPIGRA 232
           YGIRV  V PG  +     TP Y+EALA+  +   +  +EG          K   P  R 
Sbjct: 184 YGIRVNAVNPGTTQ-----TPMYDEALAFLASKREKAAKEGTEPEDNIVQGKTVSPQKRV 238

Query: 233 GKLSEVADFVCYLLSARASYITGVTTNIAGGKT 265
               EVA+ + +L S  AS ITGV   + GG T
Sbjct: 239 AAAEEVANGILFLASEEASNITGVYLPVDGGFT 271


Lambda     K      H
   0.316    0.133    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: 156
Number of extensions: 9
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: 267
Length of database: 273
Length adjustment: 25
Effective length of query: 242
Effective length of database: 248
Effective search space:    60016
Effective search space used:    60016
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: 47 (22.7 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