GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Kocuria flava HO-9041

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_058857486.1 AS188_RS02305 acyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF2392
         (383 letters)



>NCBI__GCF_001482365.1:WP_058857486.1
          Length = 398

 Score =  237 bits (605), Expect = 4e-67
 Identities = 138/380 (36%), Positives = 202/380 (53%), Gaps = 2/380 (0%)

Query: 3   DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62
           D +LS ++   RD  R+F  R I P    W +       +V +M +LGLLGM +   +G 
Sbjct: 18  DADLSPEELATRDAVREFVDRRIRPEIARWYEDAHFPREIVPEMAQLGLLGMHL-HGYGC 76

Query: 63  SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122
           +    V Y LA++E+ AGD      +S+  S+    +  +GS+ QK  WL  +A+G  IG
Sbjct: 77  AGRSAVEYGLAMQELEAGDSGLRTFVSVQGSLAMSAIAKHGSEEQKQRWLPGMAAGEIIG 136

Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182
           CF LTEP AGS+   + T A    G WVL G+K++   A  + +A+++A  D   G + +
Sbjct: 137 CFGLTEPTAGSDPSTMATTAVREGGEWVLTGAKRWIGLASIADVAVIWARADDGSGSERV 196

Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242
             FLVPTDTPGF     E K+ +RAS  C + L+  R+P   +L E   GL    S L  
Sbjct: 197 RGFLVPTDTPGFTATPIEPKLSMRASIQCDIELAGVRLPADAILPE-NPGLRGPFSCLNE 255

Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302
            R GI   ALG AR +FEAAL YA+ER+QF KP+A +Q     L DM  ++   +LL L 
Sbjct: 256 ARYGIVWGALGAARDSFEAALAYAQERIQFDKPLAAYQLTQRKLVDMALEIQKGQLLALR 315

Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362
             RLK AG       S  KL    +A ++C +A  + GG G   ++   R+  +    + 
Sbjct: 316 LGRLKDAGRLENQMISVGKLNNCRIAIEICREARTVLGGNGVTLEHSPLRHANNLESVRT 375

Query: 363 YEGSSEIQRLLIARELANYA 382
           YEG+ E+  L++ + L  +A
Sbjct: 376 YEGTDEVHTLILGQHLTGHA 395


Lambda     K      H
   0.318    0.133    0.390 

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: 352
Number of extensions: 14
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: 383
Length of database: 398
Length adjustment: 31
Effective length of query: 352
Effective length of database: 367
Effective search space:   129184
Effective search space used:   129184
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.

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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