GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pcaF in Pseudomonas fluorescens FW300-N2E2

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate Pf6N2E2_2539 3-ketoacyl-CoA thiolase (EC 2.3.1.16)

Query= SwissProt::Q8VPF1
         (401 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 3-ketoacyl-CoA
           thiolase (EC 2.3.1.16)
          Length = 394

 Score =  256 bits (654), Expect = 8e-73
 Identities = 167/412 (40%), Positives = 233/412 (56%), Gaps = 33/412 (8%)

Query: 3   REVYICDAVRTPIGR-FGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61
           REV I D+VRT + + F G     R DD+AA  V AL+ RN  ++ + +++  +G  +  
Sbjct: 2   REVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVDALLARN-DINPASVEDCIVGAGSNE 60

Query: 62  GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121
           G    N+ R   +L+ L     G+TLNR C+SG+ A+  A   IASG +++++AGGVES+
Sbjct: 61  GAQGYNIGRNVAVLSRLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120

Query: 122 SRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMP--ETADNVADDYKVSR 179
           S                 K  +T      INPL+K Q      P  +TA+ VA  Y+VSR
Sbjct: 121 SLT--------------MKSVNTD---HLINPLLKEQVPGIYFPMGQTAEIVARRYQVSR 163

Query: 180 ADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGET----------VVDADEHLRPD 229
            +QD +AL+SQQ   +AQAAG F +EI+P+ IK +  +           VVD D+  RPD
Sbjct: 164 EEQDRYALQSQQRTAKAQAAGLFDDEIIPMAIKYRVEDKNTGAVQILDGVVDRDDCNRPD 223

Query: 230 TTLEALAKLKPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAG 289
           TT E+LA LKPV   D +VTAGN+S ++DG+   ++ S E     GLK +A   G   AG
Sbjct: 224 TTYESLAGLKPVFAEDGSVTAGNSSQLSDGASMTLVISLEKALALGLKPKAFFRGFTVAG 283

Query: 290 VAPRVMGIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPN 349
             P  MGIGPV +V KLL+   L +AD D+ ELNEAFA+Q L     L I  D  + N N
Sbjct: 284 CEPDEMGIGPVFSVPKLLKAKGLQIADIDLWELNEAFASQCLYSRNRLEI--DPGKYNVN 341

Query: 350 GGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           GG+I++GHP G +G+R V   V +L++   + G+ TMCVG G G     E V
Sbjct: 342 GGSISIGHPFGMTGSRQVGHLVRELQRRNLRYGVVTMCVGGGMGATGLFEMV 393


Lambda     K      H
   0.317    0.134    0.379 

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: 391
Number of extensions: 17
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: 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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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