GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2411
          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:

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