GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Azospirillum brasilense Sp245

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate AZOBR_RS16640 AZOBR_RS16640 3-hydroxybutyrate dehydrogenase

Query= metacyc::MONOMER-20835
         (262 letters)



>FitnessBrowser__azobra:AZOBR_RS16640
          Length = 261

 Score =  126 bits (316), Expect = 5e-34
 Identities = 84/249 (33%), Positives = 128/249 (51%), Gaps = 8/249 (3%)

Query: 16  LISGGAAGIGEVLAAAYLEAGAQVHVCDVSESA-LAVFRDKYPGTVATR-----ADVSDA 69
           +++G  +GIG  +A A   AGA V +    E+A +   R         R     AD+S  
Sbjct: 9   VVTGSTSGIGLGIARALAGAGADVVLNGFGEAAAIEELRAGLAAEFGVRVGYHGADLSKP 68

Query: 70  AQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAV 129
           A+I A+     E  G +DVLVNNAGI      ++      W A I +NL+A +   HHA+
Sbjct: 69  AEIAALIGHAEETFGSVDVLVNNAGIQH-VAPVEDFPAERWDAVIALNLSAVFHGTHHAL 127

Query: 130 PMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPG 189
           P +K    G +L+IASV G +    ++ Y A K  +VGL K++A E   + +  NA+ PG
Sbjct: 128 PGMKRRGWGRILNIASVHGHVASVNKSAYVAAKHGVVGLTKTVALETAGTGVTCNAICPG 187

Query: 190 IVEGPRMDGVIRARAEQVGVPEAEMRQEYLN-KISLKRMVTAEDVAAMALFLCSPAARNV 248
            V  P +   I A A    +PE + + E L  K      VT +++  +A+FLCS +A  +
Sbjct: 188 WVLTPLVQKQIDAIASTKNIPEPQAKAELLGAKQPSGAFVTPDELGGLAVFLCSDSAAQM 247

Query: 249 TGQAISVDG 257
           TG ++ +DG
Sbjct: 248 TGASLLMDG 256


Lambda     K      H
   0.318    0.133    0.383 

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: 188
Number of extensions: 7
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: 262
Length of database: 261
Length adjustment: 25
Effective length of query: 237
Effective length of database: 236
Effective search space:    55932
Effective search space used:    55932
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: 47 (22.7 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