GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Pseudomonas simiae WCS417

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate GFF4114 PS417_21075 methylcitrate synthase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>FitnessBrowser__WCS417:GFF4114
          Length = 375

 Score =  713 bits (1840), Expect = 0.0
 Identities = 349/375 (93%), Positives = 364/375 (97%)

Query: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGEL 60
           MAEAKVLSGAGLRGQVAGQTALSTVGQ+GAGLTYRGYDVR+LAADAQFEEVAYLLLYGEL
Sbjct: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQAGAGLTYRGYDVRELAADAQFEEVAYLLLYGEL 60

Query: 61  PTQAQLDAYTGKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQDFSQQH 120
           PTQ +L AY+ KL +LRDLPQALKEVLERIPADAHPMDVMRTGCSFLGN+EPE+DFS Q 
Sbjct: 61  PTQTELAAYSAKLSKLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNIEPEKDFSVQR 120

Query: 121 DKTDRLLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHVKVMNVS 180
           D TDRLLAAFPAIMCYWYRFSH G+RI+CVTDE SIGGHFLHLLHGKKPSELHVKVMNVS
Sbjct: 121 DVTDRLLAAFPAIMCYWYRFSHDGKRIDCVTDEPSIGGHFLHLLHGKKPSELHVKVMNVS 180

Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240
           LILYAEHEFNASTFTARVCASTLSDL+SC+TAAIGSLRGPLHGGANEAAMEMIERFSS +
Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTAAIGSLRGPLHGGANEAAMEMIERFSSAE 240

Query: 241 EAIEGTLGMLARKDKIMGFGHAIYKDNDPRNEVIKGWSKKLADEVGDTVLFPVSEAIDKT 300
           EA+EGTLGMLARKDKIMGFGHAIYKD+DPRNEVIKGWSKKLADEVGD VLFPVSEAIDKT
Sbjct: 241 EAVEGTLGMLARKDKIMGFGHAIYKDSDPRNEVIKGWSKKLADEVGDKVLFPVSEAIDKT 300

Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360
           MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE
Sbjct: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360

Query: 361 YTGVEQRKFVPIEQR 375
           YTGVEQRKFVPIE+R
Sbjct: 361 YTGVEQRKFVPIERR 375


Lambda     K      H
   0.321    0.135    0.406 

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: 598
Number of extensions: 8
Number of successful extensions: 1
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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 (21.9 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