GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N2E2

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Pf6N2E2_6056 Para-aminobenzoate synthase, aminase component (EC 2.6.1.85)

Query= curated2:P05378
         (462 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6056
          Length = 447

 Score =  246 bits (627), Expect = 1e-69
 Identities = 151/362 (41%), Positives = 202/362 (55%), Gaps = 5/362 (1%)

Query: 96  PFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEPEVVAVFDHLKNLLHLVAPGRD 155
           PF GGV+GY +YD  R+ E LPS   DDL LPD  F   +   V DH      LV     
Sbjct: 88  PFAGGVIGYLSYDFGRHLETLPSHAKDDLQLPDARFGVYDWALVSDHQAGTSQLVFHPHC 147

Query: 156 PEEAEARLFWAERRLKGPLPGVPGERAGGRARFQADFSREAYLEAVRRALDYIRAGDIFQ 215
            E+   RL     +      GV             D S EAY +A  R   YI+AGD +Q
Sbjct: 148 GEDERQRLIALFSQPTAASVGV----FSLEGPMTPDLSAEAYRQAFERIQAYIQAGDCYQ 203

Query: 216 VVLSLRLSSPLTVHPFALYRALRSVNPSPYMGYLDLGEV-VLVSASPESLLRSDGRRVVT 274
           V  + R  +P     +A Y+ALR+  P+P+ G+  L +   ++S SPE  ++    +V T
Sbjct: 204 VNFAQRFRAPCQGDAWAAYQALRAACPTPFSGFQSLPDGGAVLSLSPERFVKVSEGQVET 263

Query: 275 RPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLLDLSRNDIGRVAAFGTVRVLEPLH 334
           RPI GTRPRG    ED   A ELL   K+ AE++M++DL RND+GR    G+VRV E   
Sbjct: 264 RPIKGTRPRGTTPSEDAAHAAELLASPKDRAENLMIVDLLRNDLGRTCRIGSVRVPELFS 323

Query: 335 VEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTVSGAPKIRAMEIIEELEPHRRGPY 394
           +E Y +V HLVS+V G LA  K  LD +A   P G+++GAPKIRAM+II+ELEP RRG Y
Sbjct: 324 LESYPNVHHLVSSVTGELAVDKDALDLIAGSFPGGSITGAPKIRAMQIIDELEPTRRGLY 383

Query: 395 GGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAGAGIVADSVPEREYEECWNKARALLKA 454
            GS  YL   G MD ++ +R+ +V  G +    G GIVADS  + EY+E   K + LL+ 
Sbjct: 384 CGSLLYLDVRGEMDSSIAIRSLLVKDGQVCCWGGGGIVADSDWQAEYQESITKVKVLLET 443

Query: 455 VE 456
           ++
Sbjct: 444 LQ 445


Lambda     K      H
   0.321    0.139    0.408 

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: 505
Number of extensions: 18
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: 462
Length of database: 447
Length adjustment: 33
Effective length of query: 429
Effective length of database: 414
Effective search space:   177606
Effective search space used:   177606
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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