GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Psychrobacter cryohalolentis K5

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase

Query= reanno::SB2B:6937192
         (389 letters)



>NCBI__GCF_000013905.1:WP_011513566.1
          Length = 384

 Score =  251 bits (640), Expect = 3e-71
 Identities = 129/374 (34%), Positives = 221/374 (59%), Gaps = 2/374 (0%)

Query: 16  VDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGVTVAEEYGGVNMGYLA 75
           ++ + D + +F   ++ P+   V  ++  P+++  +  ++GL G+T+ EEYGG+ +    
Sbjct: 8   LNQITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEE 67

Query: 76  HVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPKLISGEHIGALAMSEP 135
            V    E+ R S +     G ++ +  + +  +G EAQ+ KYLP+L SGE IG+  ++EP
Sbjct: 68  EVTLAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEP 127

Query: 136 NAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTD-LDKGPHGITAFIVE 194
           ++GSD  S+K  A K+GD YI+NG K +ITN P+A  + + A+TD  +K   GI+AFIVE
Sbjct: 128 DSGSDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVE 187

Query: 195 RGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNN-GVKVLMSGLDYERVVL 253
               G +  +   K+G +G++TC+++F++C VP + ++GG+   G K  M  LD  R+ +
Sbjct: 188 SDTPGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHI 247

Query: 254 SGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMNAAKSYVYNVARAC 313
           +    G  T  +D  + Y  ER QFG+ I  FQL+Q  LAD    + AAKS V + +R  
Sbjct: 248 AAASTGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLR 307

Query: 314 DRGETTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTS 373
           D G+    +++   ++A E+  ++A  A+Q+ GG GY+ +Y   R  RD +LY +  GT+
Sbjct: 308 DEGKDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTT 367

Query: 374 EIRRMLIGRELFNE 387
           +I++++I R +  E
Sbjct: 368 QIQQIIIARNMIKE 381


Lambda     K      H
   0.318    0.137    0.396 

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: 385
Number of extensions: 17
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: 389
Length of database: 384
Length adjustment: 30
Effective length of query: 359
Effective length of database: 354
Effective search space:   127086
Effective search space used:   127086
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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