GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt1d in Sphingomonas koreensis DSMZ 15582

Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate Ga0059261_2135 Ga0059261_2135 Zn-dependent alcohol dehydrogenases

Query= BRENDA::Q38707
         (365 letters)



>FitnessBrowser__Korea:Ga0059261_2135
          Length = 355

 Score =  305 bits (782), Expect = 9e-88
 Identities = 167/351 (47%), Positives = 221/351 (62%), Gaps = 7/351 (1%)

Query: 10  PVKAFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIV 69
           P  A  +AA+  T  L+PF F RR     DV + +LFCGVCHSD H   + W  T +P V
Sbjct: 2   PSPAKAYAAQSATTPLAPFSFERRDVQPDDVAIDILFCGVCHSDLHQARSEWEGTLFPCV 61

Query: 70  PGHEIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCENT--IDTY-GS 126
           PGHEIVG VT +GS V    VGD VG+GC+V SC +C SC +  E +CE T  + TY G 
Sbjct: 62  PGHEIVGRVTAIGSDVTTFAVGDLVGVGCMVDSCGTCPSCHEGEEQYCEGTGFVGTYNGP 121

Query: 127 IYFDGTMTHGGYSDTMVADEHFILR-WPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGT 185
               G  T GGYSDT+V  + F+LR       L + APLLCAGITTYSPLK++G   PG 
Sbjct: 122 DAHLGGHTFGGYSDTIVVKQGFVLRIGHDEQDLAAVAPLLCAGITTYSPLKHWGAG-PGK 180

Query: 186 KIGVVGLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGAR 245
           K+GVVG+GGLGH+ VK+A A GA V     SE KR +AL  LGA   +++ + ++M    
Sbjct: 181 KVGVVGIGGLGHMGVKIAAAMGAHVVAFTTSEGKRADAL-ALGAHEVVVSRNADEMAAHA 239

Query: 246 SSLDGIIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELP-VFSLLKGRKLLGGTING 304
            S D I++TV  +H L    +LLK +G + +VG PE     P V +L+  R+ + G++ G
Sbjct: 240 GSFDFILNTVAASHDLDAFTNLLKRDGTMTLVGVPEHAHPSPSVLNLVFRRRSIAGSLIG 299

Query: 305 GIKETQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355
           GI ETQEMLDF   H ITAD+E I +  ++ + +R+VK DV+YRFVID+A+
Sbjct: 300 GIAETQEMLDFCRDHGITADIETIAIQDIDASFDRMVKGDVKYRFVIDMAS 350


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: 362
Number of extensions: 21
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: 365
Length of database: 355
Length adjustment: 29
Effective length of query: 336
Effective length of database: 326
Effective search space:   109536
Effective search space used:   109536
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 17 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