GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Methanoculleus horonobensis T10

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_067077069.1 MCUHO_RS08885 phenylacetate--CoA ligase family protein

Query= SwissProt::Q9L9C1
         (440 letters)



>NCBI__GCF_001602375.1:WP_067077069.1
          Length = 475

 Score =  105 bits (262), Expect = 3e-27
 Identities = 97/335 (28%), Positives = 149/335 (44%), Gaps = 14/335 (4%)

Query: 11  LEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPFT 70
           L+  ++ S++EL A Q   L   + HAYENVP+YR+ F  +G+ P+D++S  DL   PF 
Sbjct: 35  LQESQRWSREELAAYQARALSRLLDHAYENVPYYRRVFRERGLVPEDIQSPEDLGLLPFL 94

Query: 71  AKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYT--LKDIDTWATVVARSIRAS 128
            + DL+ N P        +       + G+TG P    Y   +     WA +  +  R  
Sbjct: 95  TREDLQTNLPDLKARNYPDSAFEYVTTGGSTGIPVGFYYEKGVSRAREWAFMKTQWDRV- 153

Query: 129 GGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEK----QIQLIQDFKPDI 184
           G R  D   +  GY + +   G ++     G  ++  S   TE+     I  I+ FKP  
Sbjct: 154 GYRFTDRCVVLRGYTIESARDGVYWKKTLCGRWLLMSSHHMTEETLPAYIDRIKRFKPRF 213

Query: 185 IMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLS 244
           I   PS  + +   M   GI+P  T +K  + G+E      R  +    G      YG S
Sbjct: 214 IQGYPSTAVILARYMREHGIEPFPT-VKAILCGSENLYPWQRDLLTGVFGCRVFSWYGNS 272

Query: 245 EVMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIR 304
           E     +A EC E+     I+ ++   E+I  +   V   G+ GE+V T LT    P+IR
Sbjct: 273 E--QTVLAGECEESTHYH-IFPEYGIVELIGRNGQPVQGTGAMGEVVATNLTNFICPLIR 329

Query: 305 YRTRDLTRLLP---PTARSMRRMAKITGRSDDMLI 336
           YRT DL           RS   + ++ GR  D ++
Sbjct: 330 YRTMDLATAAGGPCSCGRSYPILERVEGRVQDFIV 364


Lambda     K      H
   0.318    0.137    0.406 

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: 494
Number of extensions: 22
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: 440
Length of database: 475
Length adjustment: 33
Effective length of query: 407
Effective length of database: 442
Effective search space:   179894
Effective search space used:   179894
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 (21.7 bits)
S2: 51 (24.3 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