GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO10 in Crocosphaera subtropica ATCC 51142

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate WP_009545077.1 CCE_RS17810 thiamine pyrophosphate-binding protein

Query= metacyc::MONOMER-20681
         (545 letters)



>NCBI__GCF_000017845.1:WP_009545077.1
          Length = 544

 Score =  302 bits (774), Expect = 2e-86
 Identities = 187/509 (36%), Positives = 274/509 (53%), Gaps = 18/509 (3%)

Query: 7   LLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSSTLG 66
           L+  L   G   +FG+PGDF L F K+ E++++  ++T   + A GFAADA AR    LG
Sbjct: 11  LIERLLQLGVNHVFGVPGDFVLGFNKLLEKSELEFINTCDEQGA-GFAADAYARLRG-LG 68

Query: 67  VAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDTQFQVFK 126
           V  VTY  G   + N  A  +AEKSPVVVISG+PG  E     LLHH+ +  DTQ++VF+
Sbjct: 69  VVCVTYCVGGLKIANTTAQCFAEKSPVVVISGSPGVNERTKNPLLHHKVKEFDTQYKVFQ 128

Query: 127 EITVAQARLDDPAKAPAEIARVLGAARALSRPVYLEIPRNMVN----AEVEPVGDDPAWP 182
           EITVA   LD+P  A +EI RVL AA    RPVY+EIPR+MVN    A+ +P  ++ +  
Sbjct: 129 EITVASTVLDNPDTAYSEIERVLTAALRYKRPVYIEIPRDMVNVTLGADNQPSSNNSS-- 186

Query: 183 VDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGL 242
            + DAL    +E +  +  A  PV++  VE+ R+ L+  + +L ++  +PV  T +G+ +
Sbjct: 187 SNPDALQEALEEAVNLINQAQHPVILAGVEIHRFKLQESLLKLVEKTNLPVAETLLGKSV 246

Query: 243 LADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHAFD 302
           + +     LG Y G  G     + VEESD +  LG  LSD N  +   K++ +  I    
Sbjct: 247 INEMHPNNLGIYEGAMGKEFTRKYVEESDCVIALGTFLSDVNLGIFTAKLNPQSFIDVNS 306

Query: 303 RAVTLGYHTYADIPLAGLVDALLEGLPPSDRTTRGKEPHAYPTGLQA-DGEPIAPMDIAR 361
              ++ +H Y DI L   ++ LL       R          PT      GE I    +  
Sbjct: 307 EKTSIHFHNYEDISLVDFLNGLLNA-DLKHRQVDLPSRFLLPTNFSVKPGEKITVQRLFE 365

Query: 362 AVNDRVRAGQEPLLIAADMGDCLFTAMDMI---DAGLMAPGYYAGMGFGVPAGIGAQCVS 418
            +N  +      +++ AD+GD LF   D++    +  ++P YYA +GF VPA IGAQ  +
Sbjct: 366 RLNLFI---SNDMIVIADVGDALFAGADLVVHQKSRFLSPAYYASLGFAVPASIGAQMAN 422

Query: 419 GGKRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWR 478
              R L +VGDGAFQMTG EL    R G++PI+I+ NN  +   R  Q +  FND+  W 
Sbjct: 423 STLRPLVLVGDGAFQMTGMELSTIVRYGLNPIIIVLNNLGYGTERPMQ-DGKFNDILLWN 481

Query: 479 FADMAAGM-GGDGVRVRTRAELKAALDKA 506
           ++ +      G G  +RT  EL+  L+K+
Sbjct: 482 YSQLPTIFNAGKGFDIRTEDELELGLEKS 510


Lambda     K      H
   0.321    0.137    0.405 

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: 648
Number of extensions: 27
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: 545
Length of database: 544
Length adjustment: 35
Effective length of query: 510
Effective length of database: 509
Effective search space:   259590
Effective search space used:   259590
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 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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