GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt1d in Ochrobactrum rhizosphaerae PR17

Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate WP_094573773.1 CEV32_RS01970 NAD(P)-dependent alcohol dehydrogenase

Query= BRENDA::Q38707
         (365 letters)



>NCBI__GCF_002252475.1:WP_094573773.1
          Length = 348

 Score =  329 bits (844), Expect = 6e-95
 Identities = 177/344 (51%), Positives = 221/344 (64%), Gaps = 3/344 (0%)

Query: 13  AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72
           A G+AA D    L PF F RR     DV + + +CGVCHSD H + N W    YPIVPGH
Sbjct: 4   ARGYAATDADQPLVPFTFERREPNADDVVISIQYCGVCHSDIHTVRNEWKNAVYPIVPGH 63

Query: 73  EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDG- 131
           EIVGVV+ VGS V K KVGD VG+GC V SC  C +   + E +    + TY S+  DG 
Sbjct: 64  EIVGVVSAVGSNVTKFKVGDKVGVGCFVDSCVGCATRDLDNEHYLPGLVQTYNSVDADGK 123

Query: 132 TMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVG 191
           T T GGYSD +V  E ++L  P NLPLD+ APLLCAGIT YSPL+++    PG K+ +VG
Sbjct: 124 TPTQGGYSDQIVVREGYVLSIPDNLPLDASAPLLCAGITLYSPLRHWQAG-PGKKVAIVG 182

Query: 192 LGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGI 251
           +GGLGH+ VK+A A GA VTV+  S SK+ + L KLGA  +   SD E  +    + D I
Sbjct: 183 MGGLGHMGVKLANAMGAHVTVLSQSLSKKDDGL-KLGAKEYYATSDSETFEKLAGTFDLI 241

Query: 252 IDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQE 311
           I TV V         LLK NG +V+VGAPE    +  FSL+ GRK L G++ G IKETQE
Sbjct: 242 ICTVGVAIDWNAYLGLLKVNGTMVVVGAPEDMVPVHAFSLIPGRKSLAGSMIGSIKETQE 301

Query: 312 MLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355
           MLDF  KHNI +++E I +  +N A ER++KSDVRYRFVIDIA+
Sbjct: 302 MLDFCGKHNIVSEIEKINIQDINEAYERVLKSDVRYRFVIDIAS 345


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: 332
Number of extensions: 13
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: 365
Length of database: 348
Length adjustment: 29
Effective length of query: 336
Effective length of database: 319
Effective search space:   107184
Effective search space used:   107184
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 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