GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pcaF in Pseudomonas putida KT2440

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_3754 PP_3754 Beta-ketothiolase BktB

Query= metacyc::MONOMER-15952
         (401 letters)



>lcl|FitnessBrowser__Putida:PP_3754 PP_3754 Beta-ketothiolase BktB
          Length = 394

 Score =  343 bits (879), Expect = 7e-99
 Identities = 196/401 (48%), Positives = 260/401 (64%), Gaps = 13/401 (3%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           E  ++ AVR+ IG + G+L  +   DL +   +A I R   L    V  ++ G       
Sbjct: 5   EIYVVSAVRSAIGGFGGSLKDLPLADLASAVTRAAIERSG-LAAEQVGHMVMGTVIPTEP 63

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
            +  +AR+AA+ AG+P   P   +NRLCGSGL A+ SAA+ L  G+  + +A G ESMSR
Sbjct: 64  RDAYLARVAAMNAGIPKETPAFNVNRLCGSGLQAIVSAAQGLLLGDTDVAVAAGAESMSR 123

Query: 123 APFVMGKSEQAFGRSAEI--FDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
            P+++ ++     R  ++   D T+G      ++Q  F    M  TAENV+A++ I+R  
Sbjct: 124 GPYLLPQARWG-ARMGDLQGIDYTVG------VLQDPFQHFHMGITAENVSAKYGITREM 176

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QD  AL SQ +AA AIA GR A +IVA+E+  RKG  +    DEH R D T EQLA +  
Sbjct: 177 QDELALTSQRRAARAIAEGRFASQIVALELKTRKGSVQF-SVDEHVRADVTAEQLAGMKP 235

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
            F++ G+VTAGNASG+NDGA  L+LA+ +A +R GLK  AR+VG A AGVEP +MG+GP+
Sbjct: 236 VFKKDGTVTAGNASGINDGAAGLVLATGDAVRRLGLKPLARLVGYAHAGVEPELMGLGPI 295

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVLE TGL L D+DVIE NEAFAAQ  AV RELG   D E+VNPNG  I+LGHP+G
Sbjct: 296 PATRKVLEKTGLNLQDLDVIESNEAFAAQACAVARELGF--DPEKVNPNGSGISLGHPVG 353

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
            +GA + T A+HEL+  QGRYAL TMCIG GQGIA++ ER+
Sbjct: 354 ATGAIIATKAIHELQRIQGRYALATMCIGGGQGIAVVFERV 394


Lambda     K      H
   0.319    0.134    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: 20
Number of successful extensions: 5
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: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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