GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pseudomonas stutzeri RCH2

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF2427 Psest_2475 Acyl-CoA dehydrogenases

Query= reanno::Smeli:SM_b21121
         (387 letters)



>FitnessBrowser__psRCH2:GFF2427
          Length = 392

 Score =  263 bits (672), Expect = 6e-75
 Identities = 147/380 (38%), Positives = 219/380 (57%), Gaps = 2/380 (0%)

Query: 5   GLNFALGEEIDAL-RASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEA 63
           G + A  E+   L + SVRRF  + +AP  +  +  +  P +LW  +GE GLLG+   E 
Sbjct: 8   GADCATSEDDQTLFQDSVRRFLQQEVAPHYEQWEADHQLPRALWHRLGEAGLLGVDLPEQ 67

Query: 64  HGGAGLGYLAHCVAMEEISRAS-ASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISG 122
            GG   G     +  EEISR     +   Y  H+N+ +  I+  G PAQ++ +LP++ +G
Sbjct: 68  LGGCAAGVETCLMICEEISRQGFGGLASGYNIHANIVMPYIHHLGNPAQQACWLPRMAAG 127

Query: 123 EHVGALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAG 182
           E +GA+AM+EPGAGSD+ +M+  A K    + LNGSK++ITNG  AD+++V AKTDP A 
Sbjct: 128 EVLGAIAMTEPGAGSDLAAMRASAQKVPGGWKLNGSKVFITNGLLADMVIVCAKTDPNAR 187

Query: 183 PRGITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMS 242
            RG++ FLV+   PGFS G+ + K+G   S+T+EL F D  VPE+ +LG  G+G   LM 
Sbjct: 188 ARGVSLFLVDTTLPGFSRGKAIRKIGQHASDTAELFFDDLIVPEDALLGDAGKGFAYLMQ 247

Query: 243 GLDYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARA 302
            L  ER+ ++A  +G +   L + + Y+ +R+ FGQ I +FQ  +  LA++   +   RA
Sbjct: 248 ELPRERLGVAAQAIGAIDGALQLTLDYVQQRRAFGQRIADFQNTRFTLAEVRAHLEMGRA 307

Query: 303 YVYAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAK 362
           Y         RGE +  DAA   L  +E       + +Q  GG GYT +YP  R   DA+
Sbjct: 308 YFEKCLQRYARGEMSSTDAAALKLMLSEMQCRCVDQCLQLFGGYGYTLEYPISRFYVDAR 367

Query: 363 LYEIGAGTSEIRRMLIGREL 382
           +  I AGTSEI + +I R++
Sbjct: 368 IQTIYAGTSEIMKEVIARDM 387


Lambda     K      H
   0.318    0.135    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: 328
Number of extensions: 11
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: 387
Length of database: 392
Length adjustment: 30
Effective length of query: 357
Effective length of database: 362
Effective search space:   129234
Effective search space used:   129234
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 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