GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Marinobacter adhaerens HP15

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate GFF1974 HP15_1931 2-methylcitrate synthase/citrate synthase II

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



>FitnessBrowser__Marino:GFF1974
          Length = 376

 Score =  583 bits (1504), Expect = e-171
 Identities = 283/375 (75%), Positives = 324/375 (86%)

Query: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGEL 60
           MAEAK LSGAGLRGQVAG+TAL TVG+SGAGLTYRGYD+ DLA  AQFEE+AYLLL G+L
Sbjct: 1   MAEAKQLSGAGLRGQVAGETALCTVGKSGAGLTYRGYDIADLAEKAQFEEIAYLLLRGKL 60

Query: 61  PTQAQLDAYTGKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQDFSQQH 120
           P + +LDAY  KL+ LR LP ALK VLE+IP DAHPMDVMRTGCS LGNLE E+DFS+Q 
Sbjct: 61  PNRQELDAYKKKLQSLRGLPAALKTVLEQIPKDAHPMDVMRTGCSMLGNLETEEDFSEQD 120

Query: 121 DKTDRLLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHVKVMNVS 180
           DK DR+LA FP+I+ YWYRF+H+G RIE  +D  SIGGHFL LLHGKKPSELH +VMNVS
Sbjct: 121 DKIDRMLAVFPSIITYWYRFAHEGVRIETESDVDSIGGHFLELLHGKKPSELHERVMNVS 180

Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240
           LILYAEHEFNASTFTARVCASTLSD+ SC+T AIGSLRGPLHGGANEAAM +I++F +P+
Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDIHSCVTGAIGSLRGPLHGGANEAAMALIQKFKTPE 240

Query: 241 EAIEGTLGMLARKDKIMGFGHAIYKDNDPRNEVIKGWSKKLADEVGDTVLFPVSEAIDKT 300
           EA EG +GML RK+KIMGFGHAIYK++DPRN +IK WSKKLA+EVGDTVL+PVSE  +  
Sbjct: 241 EAEEGLMGMLERKEKIMGFGHAIYKESDPRNAIIKQWSKKLAEEVGDTVLYPVSERCEAV 300

Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360
           MW +KKLF NADF+HASAYHFMGIPT+LFTPIFV SR++GW AHV EQR NNRIIRPSA+
Sbjct: 301 MWREKKLFCNADFFHASAYHFMGIPTELFTPIFVMSRVSGWTAHVKEQRENNRIIRPSAD 360

Query: 361 YTGVEQRKFVPIEQR 375
           YTG    K+VPIE+R
Sbjct: 361 YTGPADAKWVPIEER 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: 473
Number of extensions: 9
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: 376
Length adjustment: 30
Effective length of query: 345
Effective length of database: 346
Effective search space:   119370
Effective search space used:   119370
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.

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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