Alignments for a candidate for trpE in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Dyella japonica UNC79MFTsu3.2

Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate N515DRAFT_2823 N515DRAFT_2823 anthranilate synthase component 1

Query= curated2:Q9HS66
         (488 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2823
          Length = 449

 Score =  236 bits (602), Expect = 1e-66
 Identities = 175/410 (42%), Positives = 219/410 (53%), Gaps = 47/410 (11%)

Query: 80  GALDTVQAAVGA-RLARVGCD-VPHPGGLFGWLSYDIARELEAIPDTTTDARGLPRLQLG 137
           G L  + AA  A RL R   D +P  GG   +L+Y++A E+E            PRL+L 
Sbjct: 71  GFLHALDAAWQAERLPRDADDGLPFHGGWVLFLAYELAGEIE------------PRLRLA 118

Query: 138 ---VYPTIAAWREPFTPGDDLRLIAAVPVD---EYTPDGAFEAGRDRVQSLAAAIRDGDP 191
              V P   A R P          AA  VD   E T   A     D ++ +AA     D 
Sbjct: 119 PHEVLPVALALRCP----------AAAIVDHERERTVLIAEPGCEDLLEQMAA-----DL 163

Query: 192 AVGPPPADSPAPFE-SVAGRAAFESRVRRIQDAIRDGDTFQANVSHR-----LDAPAAVH 245
              PP A  PAP E        F   V RI + +  GD FQ N+S        DAP    
Sbjct: 164 EAQPPIAPLPAPLERDEDDPQLFRDGVARIHEHLHAGDIFQVNLSRAWRARFADAPT--- 220

Query: 246 PVAVFEALRDTNPAPYSGIVEFPGVDLVSASPELLLARRGRELTTEPIAGTRPRGATPAE 305
           P +++ +LR  NPAP++G+++ P   +VS+SPE L+  RG    T PIAGTRPR  TPA+
Sbjct: 221 PASLYASLRMANPAPFAGLLQQPDWAVVSSSPERLVEARGGVAQTRPIAGTRPR--TPAD 278

Query: 306 DDAARAA-LRADDKERAEHAMLVDLERNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEV 364
           D+ AR   LR   KERAEH ML+DLERNDLG+V   GSV V +   V++Y+ V H+VS V
Sbjct: 279 DELARIRELRTHPKERAEHVMLIDLERNDLGRVCVPGSVQVDELMVVESYAHVHHIVSNV 338

Query: 365 TGRLRDSCSLRDAIAAVFPGGTITGAPKPRTMALIDTVEATRRGPYTGSLAAIGFDGDAT 424
            G+LR   +    IAA FPGGTITG PK R M +I  +E   RG YTG+L  +  +GD  
Sbjct: 339 RGKLRPGVTPGQVIAATFPGGTITGCPKVRCMEIIHALEDAPRGAYTGALGYLDRNGDLD 398

Query: 425 LSITIRTLVRRAATYHLRVGAGIVHDSTPAAEYDETLAKARALVTALGDA 474
           L+I IRTL        LR GAGIV DS    E DET AKAR L+ ALG A
Sbjct: 399 LNILIRTLTLAGTQVSLRAGAGIVADSVAEKELDETRAKARGLLRALGVA 448


Lambda     K      H
   0.317    0.135    0.397 

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: 614
Number of extensions: 37
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: 488
Length of database: 449
Length adjustment: 33
Effective length of query: 455
Effective length of database: 416
Effective search space:   189280
Effective search space used:   189280
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis