GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Methanoculleus horonobensis T10

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_067075177.1 MCUHO_RS05970 phenylacetate--CoA ligase

Query= BRENDA::B4EL89
         (440 letters)



>NCBI__GCF_001602375.1:WP_067075177.1
          Length = 429

 Score =  390 bits (1002), Expect = e-113
 Identities = 204/426 (47%), Positives = 283/426 (66%), Gaps = 8/426 (1%)

Query: 14  IETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKN 73
           +ET    EL  LQL+RLKWSL  A   V  Y+R    AG+ PDD+K+L D+ K PF+ K 
Sbjct: 7   METIRSSELADLQLKRLKWSLAQA-QKVGLYQRKLKEAGISPDDIKTLDDVEKLPFTYKK 65

Query: 74  DLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPG 133
           +L+  YPFGLFAVP +++VR+H +SGTTGKPTVVGYT +D+D W+ + AR++   G    
Sbjct: 66  ELQAGYPFGLFAVPLKEIVRIHTTSGTTGKPTVVGYTRQDLDNWSELIARNMTMIGLGED 125

Query: 134 DTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYML 193
           D   NA  YGLFTGGLG HYGAE++G  V+P + G T +Q+++I DF    +  TPSY L
Sbjct: 126 DVFQNAVNYGLFTGGLGFHYGAEKIGMTVIPSATGNTRRQIEMIEDFGVTALHCTPSYAL 185

Query: 194 NLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVAC 253
           +L +  V + M     +LK GIFGAEPW++++RNE+E R+G+ A D YGLSE+ GPGVA 
Sbjct: 186 HLAE--VAESMGKTLDTLKTGIFGAEPWSESMRNELERRLGVKAYDSYGLSEMYGPGVAF 243

Query: 254 ECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTAL 313
           EC E +DG  IW D +  EIIDP TGE L  G +GELV T L K A+P++RYRT D+T L
Sbjct: 244 ECPE-RDGLHIWHDCYLVEIIDPKTGERLAPGERGELVITPLVKNALPLVRYRTGDVTRL 302

Query: 314 LPPTARAMR--RLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGHM 371
           +       R  ++ +ITGRSDDML++RG+NVFPSQIE ++ ALP +  QF + + R  H+
Sbjct: 303 MDDGCVCGRGQKIERITGRSDDMLVIRGINVFPSQIEHVLRALPEVGEQFIVYIDRVKHL 362

Query: 372 DRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKAR 431
           D + + VE+ S A  S    + A + +++   +  ++G+ + V ++  G +P    GKA+
Sbjct: 363 DEMTIEVEM-SRAGFSGELQDLARMQKKISGELHNILGLRTAVKLVEPGALP-RFEGKAK 420

Query: 432 RVIDRR 437
           RVIDRR
Sbjct: 421 RVIDRR 426


Lambda     K      H
   0.319    0.136    0.400 

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: 570
Number of extensions: 24
Number of successful extensions: 6
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: 429
Length adjustment: 32
Effective length of query: 408
Effective length of database: 397
Effective search space:   161976
Effective search space used:   161976
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: 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