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_067075175.1 MCUHO_RS05965 phenylacetate--CoA ligase

Query= SwissProt::Q72K16
         (445 letters)



>NCBI__GCF_001602375.1:WP_067075175.1
          Length = 433

 Score =  383 bits (983), Expect = e-111
 Identities = 206/439 (46%), Positives = 286/439 (65%), Gaps = 16/439 (3%)

Query: 7   LETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPFTKKT 66
           +E +P ++LR LQ + +K LV  +Y    FYRR + E  V P   R LED+ ++PF  K+
Sbjct: 8   MEEVPFDELRRLQFKLVKSLVYRLYSFNDFYRRRMKEQQVHPDDIRTLEDVAKLPFMYKS 67

Query: 67  DLRDHYPFGLFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARSLAAAGARPG 126
           DLRD YP  +F+  + E+ R H SSGTTGKPTVVGYT+ D++ ++E +AR  ++ G   G
Sbjct: 68  DLRDGYPDRIFSAEQNELVRYHVSSGTTGKPTVVGYTERDIENWSESLARGFSSCGLGRG 127

Query: 127 MMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEVISCTPSYAQ 186
            ++  +YGYGLFTGGLG H GAE +G TV+P S G TERQ+ L+QD R   I+CTPSY  
Sbjct: 128 DVMQVSYGYGLFTGGLGAHYGAERVGATVLPTSVGNTERQIELMQDLRVTAIACTPSYLL 187

Query: 187 TLAEEFRKRGVS-PEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLSEIIGPGVS 245
            + E   K GVS   +  L    LGAEPW+E +R ++++ LG+++ +IYG SE+ GP + 
Sbjct: 188 HIGEVAEKMGVSIKNDTDLRMGFLGAEPWSEQMRTRIEDWLGIRAYDIYGTSELSGP-MF 246

Query: 246 NECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLRYWTGDLTF 305
            EC E+ QG HIW D  L E+VDP TGE L  G+ G L  T L KEA+P++RY  GDLT 
Sbjct: 247 TECAEQ-QGIHIWGDLALVEIVDPATGEVLEAGEQGELTITMLQKEALPMVRYRIGDLTA 305

Query: 306 LTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHYQIVVRREG 365
           +    C CGRTH R+G I GR DDMLI+RG+NV+P+QVE  LL IP+V  H+QIVV R+G
Sbjct: 306 IEEGPCACGRTHPRIGRIRGRVDDMLIVRGINVFPSQVEHALLEIPQVGRHFQIVVDRKG 365

Query: 366 TLDEAELKVEVSEPFFREIGQEVLSDEVVEADHRLHALRERIARKIKDNVGVTLKVTLLP 425
            LD   ++VEVSE        E  SD++ E    L  +++ +  +++ ++ V++ V L+ 
Sbjct: 366 ALDSMLVRVEVSE--------EAFSDKITE----LMVIKKAVEHRLRSSLNVSVDVELVE 413

Query: 426 PGQAPRSEGGKLRRVLDLR 444
           PG  PR E GK ++V+D R
Sbjct: 414 PGTLPRFE-GKSKKVVDRR 431


Lambda     K      H
   0.319    0.139    0.409 

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: 480
Number of extensions: 16
Number of successful extensions: 4
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: 445
Length of database: 433
Length adjustment: 32
Effective length of query: 413
Effective length of database: 401
Effective search space:   165613
Effective search space used:   165613
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