GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Pedobacter sp. GW460-11-11-14-LB5

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate CA265_RS09630 CA265_RS09630 acyl-CoA dehydrogenase

Query= reanno::ANA3:7024494
         (389 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS09630 CA265_RS09630 acyl-CoA
           dehydrogenase
          Length = 396

 Score =  222 bits (565), Expect = 2e-62
 Identities = 135/380 (35%), Positives = 204/380 (53%), Gaps = 5/380 (1%)

Query: 5   YTSLNFGLGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPE 64
           Y  L+  L +E  ++R   +D+ K E++PI         FP  +   L  +G  G T+P 
Sbjct: 15  YYLLDELLTDEHKLIRATARDWVKKEVSPIIEDYAQKAEFPKHLIKGLADIGAFGPTIPV 74

Query: 65  EYGGANMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSG 124
           EYGGA + Y A+ + M+EI R  + I  +     +L +  I   G+ EQ+ KYLPKL SG
Sbjct: 75  EYGGAGLDYTAYGILMQEIERGDSGIRSTASVQGSLVMYPIYAYGSEEQRKKYLPKLASG 134

Query: 125 EHIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKG 184
           E +G   ++EP+ GS+   M  + +  G  YILNG KMWI+N P A+  V++AK +  K 
Sbjct: 135 EMMGCFGLTEPDHGSNPGGMVTNIKDAGSHYILNGAKMWISNAPFADIAVVWAKDESGK- 193

Query: 185 AHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMS 244
              I   IVERG +GFS  +   K  +R S T ELVF++V+VP+ENI   + +G+K  + 
Sbjct: 194 ---IRGLIVERGMEGFSTPETHHKWSLRASATGELVFDNVKVPKENIFPEI-SGLKGPLG 249

Query: 245 GLDYERVVLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKA 304
            L+  R  ++ G LG    C D  + Y  ER QFGK IG FQL Q KLA+M T +   + 
Sbjct: 250 CLNQARYGIAWGALGAAMDCYDTALRYSKERVQFGKPIGGFQLQQKKLAEMVTEITKGQL 309

Query: 305 YVYSVAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAK 364
            V+ +         + +  + A   S E+A  +A +A Q+LGG G   EY+  R + + +
Sbjct: 310 LVWRLGVLKSENRASAEQISMAKRNSVEIALDIARNARQMLGGMGITGEYSIMRHMMNLE 369

Query: 365 LYEIGAGTSEIRRMLIGREL 384
                 GT +I  ++ G ++
Sbjct: 370 SVVTYEGTHDIHLLITGMDV 389


Lambda     K      H
   0.316    0.135    0.388 

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: 388
Number of extensions: 15
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: 396
Length adjustment: 31
Effective length of query: 358
Effective length of database: 365
Effective search space:   130670
Effective search space used:   130670
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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