GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Pseudomonas fluorescens FW300-N1B4

Align anthranilate synthase (EC 4.1.3.27) (characterized)
to candidate Pf1N1B4_3814 Para-aminobenzoate synthase, aminase component (EC 2.6.1.85)

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3814
          Length = 445

 Score =  233 bits (593), Expect = 1e-65
 Identities = 164/460 (35%), Positives = 232/460 (50%), Gaps = 45/460 (9%)

Query: 30  PLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGLPCRTVLRVYDHQVRISIDGVETERFD 89
           P   +  +  AP + LL+S +   + GRY ++       L V   +              
Sbjct: 15  PAEYFAAIRHAPGAVLLDSGRPSAERGRYDLLSAWPLEQLAVLPDESGSHF--------- 65

Query: 90  CADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFGYDCVRYVEKRLATCPNPDPLGNPDI 149
               L  + +   R    TVP    F GGL+GY  YD  R++E   +     D L  PD 
Sbjct: 66  ----LQRLRDTLKRLGKATVPFDLPFAGGLIGYLSYDFGRHLENLPSQAR--DDLQLPDA 119

Query: 150 LLMVSDAVVVFDNLAGKIHAI---VLADPSEENAYERGQARLEELLERLRQPITPRRGLD 206
              + D  ++ D+       +    L D   +            LLE   QP        
Sbjct: 120 RFGLYDWALISDHHLATSQLVFHPALIDSERQR-----------LLELFTQP-------- 160

Query: 207 LEAAQGREP-----AFRASFTREDYENAVGRIKDYILAGDCMQVVPSQRMSIEFKAAPID 261
             A Q  EP        A  + +DY  A  RI+ YI AGDC QV  +QR   + +  P  
Sbjct: 161 --APQKIEPFKLDGPMSADLSADDYRQAFERIQQYIQAGDCYQVNFAQRFRAQCQGDPWA 218

Query: 262 LYRALRCFNPTPYMYFFNFGDFHVVGS-SPEVLVRVEDGLVTVRPIAGTRPRGINEEADL 320
            Y ALR   PTP+  F +  D   V S SPE  V+V    V  RPI GTRPRG+    D 
Sbjct: 219 AYCALRAACPTPFSGFQSLPDGDAVLSLSPERFVKVSGRHVETRPIKGTRPRGLTAAEDA 278

Query: 321 ALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERYSNVMHIVSNVTGQ 380
           A   +LL+  K+ AE+LM++DL RND+GR   IG+V+V E   +E Y NV H+VS+VTG+
Sbjct: 279 ANAAELLASPKDRAENLMIVDLLRNDLGRTCRIGSVRVPELFSLESYPNVHHLVSSVTGE 338

Query: 381 LREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYLAWNGNMDTAI 440
           L +   A+D +    P G+++GAPKIRAM+IIDELEP +RG+Y G++ YL   G MD++I
Sbjct: 339 LADDKDALDLIAGSFPGGSITGAPKIRAMQIIDELEPTRRGLYCGSLLYLDVRGEMDSSI 398

Query: 441 AIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480
           AIR+ ++K+G++    GGGIVADS    E++E+I K + +
Sbjct: 399 AIRSLLVKDGQVCCWGGGGIVADSDWQAEYQESITKVKVL 438


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: 528
Number of extensions: 27
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 492
Length of database: 445
Length adjustment: 33
Effective length of query: 459
Effective length of database: 412
Effective search space:   189108
Effective search space used:   189108
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