GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Moritella dasanensis ArB 0140

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_017220074.1 A923_RS0102530 acetyl-CoA C-acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_000276805.1:WP_017220074.1
          Length = 404

 Score =  265 bits (677), Expect = 2e-75
 Identities = 171/423 (40%), Positives = 235/423 (55%), Gaps = 48/423 (11%)

Query: 3   EAFICDGIRTP--IGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           +AFI D IRTP  +G+  GAL  V+  +L A  L  L  RN   D + +DD++LGC    
Sbjct: 4   QAFIYDAIRTPRGLGKPSGALHEVKPVNLLADLLNHLQARNG-FDTDAVDDIVLGCVTPI 62

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           G+   ++A+ A L+AG   +V+G +INR C SGL+++  AA  I++G   L+IAGGVESM
Sbjct: 63  GDQGADIAKTAALVAGWKDNVAGVSINRFCASGLESVNMAAMKIRSGWEHLVIAGGVESM 122

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPET--AENVAELLKISR 178
           SR    MG    A+S   E                    TD MP+   A+ +A L   SR
Sbjct: 123 SRVK--MGADGGAWSMDPET----------------SLATDYMPQGIGADLIATLDGYSR 164

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
           ED D FA RS QR A A   G   + +VPV  +N  G++  +  D+ +R + ++  L  L
Sbjct: 165 EDVDEFAARSHQRAAAAWQRGAFDKSVVPVCDRN--GMLL-LDKDQLVRADCSITSLAQL 221

Query: 239 KAPFRANG--------------------VITAGNASGVNDGAAALIIASEQMAAAQGLTP 278
           K  F   G                    V T GNASG+ DGAA +++ S +     GL P
Sbjct: 222 KPAFAYIGQTTFDSVAKRRYPQVCQIQHVHTPGNASGIVDGAALVLVGSAEAGVKWGLKP 281

Query: 279 RARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELG 338
           RARIVA A  G +P +M  GPVPAT++ L  AGL+I+D+D+ E+NEAFAA  +  + EL 
Sbjct: 282 RARIVATAVVGADPTIMLTGPVPATKKALAVAGLTINDIDLFEVNEAFAAVVMRFMNELN 341

Query: 339 LPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMIL 398
           +  D   VN NGG+IA+GHPLG +GA +  +   EL  RN +  L T+C+G G GIA I+
Sbjct: 342 ISPDI--VNVNGGSIAMGHPLGATGAIILGSLLDELETRNLKRGLATLCVGGGMGIATII 399

Query: 399 ERV 401
           ERV
Sbjct: 400 ERV 402


Lambda     K      H
   0.319    0.135    0.384 

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: 436
Number of extensions: 19
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: 401
Length of database: 404
Length adjustment: 31
Effective length of query: 370
Effective length of database: 373
Effective search space:   138010
Effective search space used:   138010
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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