GapMind for catabolism of small carbon sources

 

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

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_084199172.1 C0029_RS09065 acyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF2397
         (379 letters)



>NCBI__GCF_002869505.1:WP_084199172.1
          Length = 378

 Score =  269 bits (687), Expect = 1e-76
 Identities = 143/377 (37%), Positives = 216/377 (57%), Gaps = 1/377 (0%)

Query: 2   LPNEDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSD 61
           + NE+     +MAR+  ++ ++P  E W  +H  P E    + A G     +PE +GG+ 
Sbjct: 1   MDNEELTLFRDMARRAYEQEIEPHYEGWEEQHLVPRELWNTLGAAGLLCPDMPEAYGGAG 60

Query: 62  TGYLAYAMALEEIAA-GDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGA 120
           T        +EE++  G G  ++   +H+++    I  FG E+QK  +L  +  GE +GA
Sbjct: 61  TSPRVCLAMIEEMSRMGFGGLASGYGIHSNIVAPYINHFGTEEQKQQWLPKMITGEAVGA 120

Query: 121 FALTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGIS 180
            A+TEP AGSD   +RT A RDG+ +VLNG+K FIT+G HA  VIV A+TDP  G  G S
Sbjct: 121 LAMTEPGAGSDVQGIRTTAVRDGEEWVLNGSKIFITNGIHADLVIVAAITDPGKGAKGTS 180

Query: 181 AFIVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGG 240
            F+V    PG++     +K+GQHASDT ++ F+D+R+P +  LGEE +G+ I +  L   
Sbjct: 181 LFLVDASLPGFEKGNKIEKIGQHASDTAELFFQDVRLPASALLGEENKGFVIMMTELPRE 240

Query: 241 RIGIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHA 300
           R+GIAAQAV  A  A +   DY  +R+ FG+ +   Q   F LA++ T+IA+ R +    
Sbjct: 241 RLGIAAQAVAAAEGAMDITVDYVLERKAFGQTVASFQNTRFTLAEVKTEIALNRALYEKC 300

Query: 301 AALREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIY 360
           A     G     +A+M K   +EM        +Q  GGYGY A++P+ R Y D R+ +IY
Sbjct: 301 ADDYARGELTADDAAMLKYANTEMQCSTIDQCLQLFGGYGYTAEYPISRYYTDARIQRIY 360

Query: 361 EGTSDIQRLVISRNLGG 377
            GTS+I R +++R++ G
Sbjct: 361 GGTSEIMRELVARSILG 377


Lambda     K      H
   0.320    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: 379
Number of extensions: 15
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: 379
Length of database: 378
Length adjustment: 30
Effective length of query: 349
Effective length of database: 348
Effective search space:   121452
Effective search space used:   121452
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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