GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Halioglobus japonicus S1-36

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_084199172.1 C0029_RS09065 acyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF1051
         (387 letters)



>NCBI__GCF_002869505.1:WP_084199172.1
          Length = 378

 Score =  270 bits (689), Expect = 7e-77
 Identities = 146/372 (39%), Positives = 212/372 (56%), Gaps = 1/372 (0%)

Query: 12  ETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGY 71
           E + + R+  +     EI P  E  ++++L P ++W   G  GLL   + E YGGAG   
Sbjct: 4   EELTLFRDMARRAYEQEIEPHYEGWEEQHLVPRELWNTLGAAGLLCPDMPEAYGGAGTSP 63

Query: 72  LAHVVAMEEISR-GSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAM 130
              +  +EE+SR G   +A  YG HSN+    IN  G  EQK ++LPK+I+GE VGALAM
Sbjct: 64  RVCLAMIEEMSRMGFGGLASGYGIHSNIVAPYINHFGTEEQKQQWLPKMITGEAVGALAM 123

Query: 131 SEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFI 190
           +EP AGSDV  ++  A + G+ +VLNGSK +ITNG  A+  ++ A TD  KGA G + F+
Sbjct: 124 TEPGAGSDVQGIRTTAVRDGEEWVLNGSKIFITNGIHADLVIVAAITDPGKGAKGTSLFL 183

Query: 191 VERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLDYERVV 250
           V+    GF +GNK +K+G   S+T ELFF DV +P   +LG EN G  ++M+ L  ER+ 
Sbjct: 184 VDASLPGFEKGNKIEKIGQHASDTAELFFQDVRLPASALLGEENKGFVIMMTELPRERLG 243

Query: 251 LAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQA 310
           +A       +  +D+ V Y+ +RK FGQ++  FQ  +  +A++ T++  +RA     A  
Sbjct: 244 IAAQAVAAAEGAMDITVDYVLERKAFGQTVASFQNTRFTLAEVKTEIALNRALYEKCADD 303

Query: 311 CDRGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEIGAGT 370
             RGE T  DAA +     E       Q +Q+ GG GY  E+P  R   DA++  I  GT
Sbjct: 304 YARGELTADDAAMLKYANTEMQCSTIDQCLQLFGGYGYTAEYPISRYYTDARIQRIYGGT 363

Query: 371 SEIRRMLIGREL 382
           SEI R L+ R +
Sbjct: 364 SEIMRELVARSI 375


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: 396
Number of extensions: 21
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: 378
Length adjustment: 30
Effective length of query: 357
Effective length of database: 348
Effective search space:   124236
Effective search space used:   124236
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.

Links

Downloads

Related tools

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