GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pcaF in Pseudomonas fluorescens GW456-L13

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_2411 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2411
           3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA
           acetyltransferase (EC 2.3.1.9)
          Length = 393

 Score =  324 bits (831), Expect = 2e-93
 Identities = 189/400 (47%), Positives = 250/400 (62%), Gaps = 12/400 (3%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           E  ++ A RT IG + G+L  V   DL    +KA + R   +D + V  ++ G       
Sbjct: 5   EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALER-AAVDPALVGHLVMGNVIPTET 63

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
            +  ++R+AA+ AG+P   P   +NRLCGSGL A+ +AA+ L  G+A +++  G ESMSR
Sbjct: 64  RDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSR 123

Query: 123 APFVMGKSEQAFGR-SAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQ 181
            P++M  +       +A++ D  +G      ++   F    M  TAENVAA+  I+R  Q
Sbjct: 124 GPYLMPAARWGSRMGNAQVIDYMLG------ILHDPFHGIHMGITAENVAARNGITREMQ 177

Query: 182 DAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTP 241
           DA A   Q +AA AIANG  +++I  VEI  RKG  K+   DEHPR  T+LEQLA +   
Sbjct: 178 DALAFEDQQRAAHAIANGYFSEQIATVEIQDRKG-VKLFSVDEHPRA-TSLEQLAAMKPA 235

Query: 242 FRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVP 301
           F++ GSVTAGNASG+NDGA AL++AS  A Q + LK  AR+V  A AGVEP  MG+GP+P
Sbjct: 236 FKKDGSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIP 295

Query: 302 ATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGM 361
           ATR  L+  GL +AD+DVIE N AFAAQ  AV +EL L  D  +VNPNG  IALGHP+G 
Sbjct: 296 ATRLALKRAGLTVADLDVIEANIAFAAQACAVSQELDL--DPAKVNPNGSGIALGHPVGA 353

Query: 362 SGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           +GA + T A+HEL    GRYAL TMCIG GQGIA I ER+
Sbjct: 354 TGAIIATKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393


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: 404
Number of extensions: 23
Number of successful extensions: 4
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: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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.

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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 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