GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pseudomonas fluorescens FW300-N2C3

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate AO356_03560 AO356_03560 acetyl-CoA acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_03560
          Length = 394

 Score =  254 bits (649), Expect = 3e-72
 Identities = 166/412 (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   REVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVNALLARN-DINPASVEDCIVGAGSNE 60

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

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

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

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

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

Query: 350 GGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           GG+I++GHP G +G+R V   V +L++   + G+ TMCVG G G     E V
Sbjct: 342 GGSISIGHPFGMTGSRQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFEAV 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: 380
Number of extensions: 16
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 (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