GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS09630
          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:

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