GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Desulfovibrio vulgaris Hildenborough

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 209425 DVU0489 phenylacetate-coenzyme A ligase

Query= SwissProt::P76085
         (437 letters)



>MicrobesOnline__882:209425
          Length = 432

 Score =  327 bits (837), Expect = 6e-94
 Identities = 187/426 (43%), Positives = 254/426 (59%), Gaps = 12/426 (2%)

Query: 16  DELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDLRKFPCTTKQDLRDNY 75
           ++L A+Q + L+WT++HAYE  P YR K  AAGV PDD   L D+R+ P TT  DLRD+Y
Sbjct: 14  EKLHAIQLEGLRWTVRHAYEGSPRYRAKLRAAGVVPDDIVHLDDVRRLPFTTVADLRDDY 73

Query: 76  PFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARSLRAAGGSPKDKIHVA 135
           P    +VP + VVRIHASSGTTGK  ++ YTQ D+D +A  +AR    AG + +D++ +A
Sbjct: 74  PLPLLSVPEKDVVRIHASSGTTGKRKILAYTQRDVDTFALQMARCYELAGLTQEDRVQIA 133

Query: 136 YGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDMIMVTPSYCLNLIEEL 195
            GYGL+T G G   G ER GA  +P+  G  E Q QL+ D     +  T S  L + EE+
Sbjct: 134 VGYGLWTAGAGFQLGCERFGALTVPVGPGNLEMQLQLLTDLGVTCLCSTASMALLMAEEV 193

Query: 196 ERQ-LGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGIT-ALDIYGLSEVMGPGVAMECL 253
           ER  L GD     LR  +FGAE  +  MR+  E +LG+  + DI G++E+ GPG  +EC 
Sbjct: 194 ERHGLRGD---IRLRKVIFGAEAHSAKMRRTFEEKLGLEGSFDIAGMTEMYGPGTGLEC- 249

Query: 254 ETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVIRYRTRDLTRLLPG 313
           E  DG   W D F  EI++P    P+  GE GE++ T+L KEA P+IRYRTRDLTRL+PG
Sbjct: 250 EAHDGIHYWADLFLVEILDPETLQPVEPGEVGEMVVTSLRKEASPLIRYRTRDLTRLIPG 309

Query: 314 T---ARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQLEVNRRGHLDS 370
           T    R + R D I GRSDDM+I RGVN++P Q+ + +  F  +   Y +E+ R+   D 
Sbjct: 310 TCSCGRNIPRHDHILGRSDDMIIFRGVNIYPGQIADVLHLFPEVGSEYHIELTRKEGRDH 369

Query: 371 LSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPRSEGKACRVFD 430
           + +KVE +  + T              HR K M  +S  V +V  G +PRS  K+ RV D
Sbjct: 370 MLLKVERQPGAATGDERTLGVAIGNELHR-KLMARVS--VAVVAPGELPRSFAKSKRVTD 426

Query: 431 LRNIVG 436
           LR + G
Sbjct: 427 LRMVEG 432


Lambda     K      H
   0.320    0.137    0.411 

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: 498
Number of extensions: 22
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: 437
Length of database: 432
Length adjustment: 32
Effective length of query: 405
Effective length of database: 400
Effective search space:   162000
Effective search space used:   162000
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 17 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