GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Ochrobactrum rhizosphaerae PR17

Align Alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_094578795.1 CEV32_RS19735 alcohol dehydrogenase AdhP

Query= reanno::Cup4G11:RR42_RS34260
         (342 letters)



>NCBI__GCF_002252475.1:WP_094578795.1
          Length = 344

 Score =  541 bits (1393), Expect = e-158
 Identities = 265/341 (77%), Positives = 294/341 (86%), Gaps = 2/341 (0%)

Query: 1   MTAMMKAAVVREFGAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLP 60
           M   MKAAVVREFG PLTIDEVP+PQPG GQIQV I+ASGVCHTDLHAAEGDWPVKP  P
Sbjct: 1   MAKTMKAAVVREFGKPLTIDEVPIPQPGDGQIQVAIQASGVCHTDLHAAEGDWPVKPNPP 60

Query: 61  FIPGHEGVGYVSAVGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120
           FIPGHEGVG+VSAVG GV  VKEGDRVG+PWLY+ACG+C HCL GWETLCE+Q NTGYSV
Sbjct: 61  FIPGHEGVGFVSAVGKGVKHVKEGDRVGIPWLYTACGHCVHCLGGWETLCEEQLNTGYSV 120

Query: 121 NGGYGEYVVADPNYVGLLPDSVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180
           NGG+ +YVVADPN+VG LP ++ F EIAPILCAGVTVYKGLKVTDT+PG WVVISGIGGL
Sbjct: 121 NGGFADYVVADPNFVGHLPKNIEFNEIAPILCAGVTVYKGLKVTDTKPGDWVVISGIGGL 180

Query: 181 GHVAVQYARAMGLRVAAVDIDDKKLELARKLGAEVTVNART-TDPVAFLQKEI-GGAHGA 238
           GH+AVQYA+AMGL VAAVDIDDKKL+LAR+LGA VTVNA+T  DP A+++KE  GGA G 
Sbjct: 181 GHMAVQYAKAMGLNVAAVDIDDKKLDLARRLGATVTVNAKTHNDPAAYIKKETDGGAQGV 240

Query: 239 LVTAVSPKAFGQAIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQE 298
           LVTAVSPKAF QAIGM  RGGTIALNGLP GDFP  IF++VL G+T+RGSIVGTR DLQE
Sbjct: 241 LVTAVSPKAFEQAIGMAARGGTIALNGLPAGDFPLSIFNMVLNGVTVRGSIVGTRLDLQE 300

Query: 299 SLDFAAHGAVKATVSTAPLEKINEIFTRMRAGDIEGRVVMD 339
           S+DFAA G VKAT+ T  ++ IN IF  MRAG IEGRVVMD
Sbjct: 301 SIDFAADGKVKATIRTDKIDNINAIFDEMRAGQIEGRVVMD 341


Lambda     K      H
   0.319    0.138    0.420 

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: 464
Number of extensions: 13
Number of successful extensions: 2
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: 342
Length of database: 344
Length adjustment: 29
Effective length of query: 313
Effective length of database: 315
Effective search space:    98595
Effective search space used:    98595
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