Alignments for a candidate for mt2d in Dyadobacter tibetensis Y620-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mt2d in Dyadobacter tibetensis Y620-1

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_025763732.1 X939_RS0113100 mannitol dehydrogenase family protein

Query= BRENDA::O08355
         (493 letters)



>NCBI__GCF_000566685.1:WP_025763732.1
          Length = 497

 Score =  417 bits (1071), Expect = e-121
 Identities = 222/489 (45%), Positives = 300/489 (61%), Gaps = 7/489 (1%)

Query: 3   LNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICG 62
           LN+ NL +L   VK+P+Y   + +  I HIGVG FHR+H+A+YT+ LM     LD  ICG
Sbjct: 7   LNQDNLGKLPARVKVPSYNRDEVKTSIVHIGVGNFHRSHEAFYTNELMERHGILDCGICG 66

Query: 63  VGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASP 122
           VGL   DR+  + L  QD L+TL           RVIGSI + + A ++  A+I+K+ASP
Sbjct: 67  VGLLDYDRRIYNILKDQDGLYTLVVKELDGSKSARVIGSIVEFMFAPENPIAVIEKMASP 126

Query: 123 EIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIP 182
           +I+I+SLTITEGGY ++++ GEF    P I  D+ +P SPKTVFG++  AL  R   G+ 
Sbjct: 127 DIKIISLTITEGGYNLNEATGEFDFSNPVIIQDMKNPLSPKTVFGYLAQALKLRMNRGVG 186

Query: 183 AFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRL 242
             T+ SCDN+  NG V +KAL+ +       L  WI+ +VSFPNAMVDRITP+T T    
Sbjct: 187 GCTIQSCDNIQGNGHVAKKALINYVRHAEPALEAWIEENVSFPNAMVDRITPVTLTDDIE 246

Query: 243 QLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGS 302
            L  E  ++D WPVVCEPF+QWV+ED F  GRPAWEKVGVQF +DV PYE MK+ LLN  
Sbjct: 247 NLQQEFLVEDQWPVVCEPFIQWVIEDDFAAGRPAWEKVGVQFVNDVLPYENMKLRLLNAG 306

Query: 303 HLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRF 362
           H  L  LG L GY+ + E  +DP F  +++ +MD +V+P L  + GI+L DYK++LV RF
Sbjct: 307 HSVLGMLGALHGYKTIDEAASDPDFSNFLKDFMDKEVSPTLGDLGGINLDDYKKSLVARF 366

Query: 363 SNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGV 422
            N  I D + R+C + S+K P F +PT+   +       RAA +VAAW  Y  G+DENG 
Sbjct: 367 QNVHIKDMIARICLESSAKIPIFLLPTVKSQLKQEGNISRAAFIVAAWCKYNDGIDENGN 426

Query: 423 SYTIPDPRAEFCQGLVSDDALISQ---RLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDN 479
           +Y I D  +     L+   AL  Q   R L ++ IFG  + N+  FV AF R    LR +
Sbjct: 427 TYPIEDAMS---NELIRAAALSHQLPIRFLEIKSIFGDLV-NNEAFVQAFLRSLSLLRSH 482

Query: 480 GVTTTLKHL 488
            V   +K +
Sbjct: 483 KVKECVKQI 491


Lambda     K      H
   0.321    0.137    0.414 

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: 575
Number of extensions: 30
Number of successful extensions: 1
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: 493
Length of database: 497
Length adjustment: 34
Effective length of query: 459
Effective length of database: 463
Effective search space:   212517
Effective search space used:   212517
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources