GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Burkholderia phytofirmans PsJN

Align Lmo2664 protein (characterized, see rationale)
to candidate BPHYT_RS23440 BPHYT_RS23440 alcohol dehydrogenase

Query= uniprot:Q8Y413
         (350 letters)



>FitnessBrowser__BFirm:BPHYT_RS23440
          Length = 348

 Score =  148 bits (374), Expect = 2e-40
 Identities = 107/350 (30%), Positives = 175/350 (50%), Gaps = 29/350 (8%)

Query: 1   MRAAVLYENNVIKAEQIDEATCGKDQVRVEVKAVGICGSDIHKM----QTRWKYPLPAVM 56
           M AAVL+E  +I+ +++D    G  +VRV V+A GICGSD+          +    P V+
Sbjct: 1   MLAAVLHEPKLIRIDEVDPPEPGPGEVRVRVRAGGICGSDLSYYFKGKSGDFAVREPFVL 60

Query: 57  GHEFAGVITEIGSEVT---NVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGS--- 110
           GHE AG I  +G  VT    +A G RVA  P   C  C +C  G    C N R +GS   
Sbjct: 61  GHEVAGEIDSLGEGVTAERRLAPGQRVAVNPGLACGTCRFCVGGMPNHCLNMRFMGSAST 120

Query: 111 --HFHGGFAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGI 167
             H  G F + +V+ A   + + D +DF + +M EPLAV++H V      +G +V++ G 
Sbjct: 121 FPHTQGMFRQYIVVAARQCVPVPDGVDFAQASMAEPLAVALHAVKQAGSLVGASVLLVGC 180

Query: 168 GTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLG 227
           G IG +++     AG   ++A+D+SD+ L  AR+ G   T+N     + ++ ++   G  
Sbjct: 181 GPIGCILLSVARRAGAHRVVALDLSDRALQVARQLGADQTVNAAERAVIDQ-WSVQRGT- 238

Query: 228 ADIALECAGSKITQEQCLLVTKKKG---KVGFLGIAYADVLLHEEAFENIFRRELTLKGF 284
            D+ +E +GS    +  L   +  G   +VG L    + V     A   +  +EL  +G 
Sbjct: 239 FDVVIEASGSPAGLDTALHAARAGGTVIQVGNLPAGQSPV-----AANLVMSKELRYQGS 293

Query: 285 WNSYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSR 334
           +   S      E+  + + +  G++ L+PL++H + + E   AF++ L R
Sbjct: 294 FRFTS------EYAIAADEIASGKVDLRPLMTHAFAMSEANRAFEVALDR 337


Lambda     K      H
   0.321    0.139    0.417 

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: 249
Number of extensions: 12
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: 350
Length of database: 348
Length adjustment: 29
Effective length of query: 321
Effective length of database: 319
Effective search space:   102399
Effective search space used:   102399
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: 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