GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Salinicoccus carnicancri Crm

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein

Query= BRENDA::Q6ECH5
         (336 letters)



>NCBI__GCF_000330705.1:WP_017549841.1
          Length = 338

 Score =  147 bits (372), Expect = 3e-40
 Identities = 98/324 (30%), Positives = 166/324 (51%), Gaps = 14/324 (4%)

Query: 1   MEALVLTGKKQLEIEDIKEPEIKP-DEVLIHTAYAGICGTDKALYAGLPGSASAVPPIVL 59
           M+A+ +    QL I ++++P I+  DEV++     GICG+D  +Y G     S   P V+
Sbjct: 1   MKAIQVEKPGQLNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNPFTSY--PRVI 58

Query: 60  GHENSGVVTKVGSEVTNVKPGDRVTVDPNIYCGQCKYCRTQRPELCEHLDAVGVTRNGGF 119
           GHE SG+V +VG  VT++ PGD V ++P  YCG+C  CR  +P +C+ L+  GV R+GG 
Sbjct: 59  GHEVSGIVEQVGEAVTSLAPGDLVALEPITYCGECYACRNGQPNVCDSLEVFGVHRDGGM 118

Query: 120 EEYFTAPAKVVYPIPDDVSLKAAAVVEPISCAMHGVDLLETHPYQKALVLGDGFEGQLFA 179
            EY  A     + +P +VS +AAA++EP++         +        V+G G  G    
Sbjct: 119 AEYLKADENNWHKVPGNVSEEAAALMEPMTIGAQATYRGDVREGDTVFVIGAGPTGIACL 178

Query: 180 QILKARGIHEVTLAGRSDEKLENNRKHFGVKTIDT----TKEEI----PADAYDIVVEAV 231
              K RG  +V ++  +  +L+  +      TI       +EEI      +  ++V++AV
Sbjct: 179 LQAKQRGA-KVFISDFNQNRLDYAKSIGADATIQPDGVHVEEEINRLTNGELANVVIDAV 237

Query: 232 GLPATQEQALAAAARGAQVLMFGVGNPDDKFSVNTYDVFQKQLTIQGAFVNPYTFEDSIA 291
           GLP T +QA+  A+   +V+  G    +   S+ +  + +K+L + G+ +  + F   I 
Sbjct: 238 GLPQTFQQAVELASIAGRVVTLGFN--EQPSSIPSLLLTKKELKVAGSRLQTHQFPKVID 295

Query: 292 LLSSGVVDPLPLFSHELDLDGVED 315
            +  G +DP  + S    +D + D
Sbjct: 296 QVGRGEIDPTQIISQRYSMDQIHD 319


Lambda     K      H
   0.316    0.136    0.393 

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: 263
Number of extensions: 15
Number of successful extensions: 3
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: 336
Length of database: 338
Length adjustment: 28
Effective length of query: 308
Effective length of database: 310
Effective search space:    95480
Effective search space used:    95480
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