GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Thiothrix lacustris DSM 21227

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>NCBI__GCF_000621325.1:WP_211248857.1
          Length = 255

 Score =  113 bits (283), Expect = 3e-30
 Identities = 77/251 (30%), Positives = 123/251 (49%), Gaps = 15/251 (5%)

Query: 12  GLRVLISGAAAGIGAAIAQAFLDVGANVYI----CDVDPAAIDRARTAHPQLHAGVADVS 67
           G  V+I+GA++GIG A A AF   G  + +     +   A     R    +      DV 
Sbjct: 11  GKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEAVAAAIRATGGEAVFVCTDVL 70

Query: 68  DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127
             A + R++  A    GGLD+L NNAG  G + A  +   AE++ T+ TN+ S  + ++ 
Sbjct: 71  QEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSVLWGMQH 130

Query: 128 AVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAI 187
           A+  ++  SA   II  AS+   +G+A    Y+ASK A+VGM +  A+E     +R+NA+
Sbjct: 131 AIRAMQ--SAGGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQGIRINAV 188

Query: 188 LPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQ 247
            PG+       R+         +G +  +  ++      R     ++AA  +FLAS    
Sbjct: 189 CPGITYTPMSQRL---------LGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNAS 239

Query: 248 NISGQAISVDG 258
            ISGQ ++VDG
Sbjct: 240 YISGQCLNVDG 250


Lambda     K      H
   0.320    0.136    0.391 

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: 143
Number of extensions: 5
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: 263
Length of database: 255
Length adjustment: 24
Effective length of query: 239
Effective length of database: 231
Effective search space:    55209
Effective search space used:    55209
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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