GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Nocardiopsis lucentensis DSM 44048

Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_017597380.1 D471_RS0103705 anthranilate synthase component I

Query= BRENDA::P00897
         (519 letters)



>NCBI__GCF_000341125.1:WP_017597380.1
          Length = 457

 Score =  172 bits (437), Expect = 2e-47
 Identities = 130/407 (31%), Positives = 201/407 (49%), Gaps = 25/407 (6%)

Query: 54  IDSALPITALGHTVSVQALTANGPALLPVLDEALPPEVRNQARPNGRE---LTFPAIDAV 110
           +D  L + A G  V+  AL A G  LLPV+ +AL      Q R    +   +T P  DA 
Sbjct: 64  VDPCLEVIARGRRVTATALNARGRVLLPVVADALVSVGAGQDREADADHVAVTVPEPDAG 123

Query: 111 Q--DEDARLRSLSVFDALRTLLTLVDSPADEREAVMLGGLFAYDLVAGFENLPA-VRQDQ 167
           +   E+ R R  SVF A+R ++  + SP D    + L G F YDL   FE + A + +D 
Sbjct: 124 EFFTEEERSRRPSVFTAVRAVIAAMSSPEDAN--LGLYGAFGYDLAFQFEPIEAHIDRDP 181

Query: 168 RCPDFCFYLAETLLVLDHQRGSARLQASVFSEQASEAQRLQHRLEQLQAELQQPPQPIPH 227
              D   +L + ++V D +R +       F+  A +  R +   + L+   +  P+ +  
Sbjct: 182 GDRDLVLHLPDAIVVRDRKRETCVRYTYEFTVPA-DGDRPEASTDGLERVTEPTPRVVAA 240

Query: 228 QKLENMQLSCNQSDEEYGAVVSELQEAIRQGEIFQVVPSRRFSLPCPAPLGPYQTLKDNN 287
           +  E  +         Y  VV+E +E  R+G++F+VVP  R    C +P   Y+ L++ N
Sbjct: 241 EVPEGPEPG------SYARVVAEAKEKFRRGDLFEVVPGHRTYARCSSPARFYELLRERN 294

Query: 288 PSPYMFFMQ-DDDFTLFGASPESALKYDAG---NRQIEIYPIAGTRPRGRRADGSLDLDL 343
           P+PY FF    +   L GASPE  ++        +++E  PI+GT  RG  A G      
Sbjct: 295 PAPYEFFFNLGEGEYLVGASPEMFVRVTGEPGTGQRVETCPISGTISRGEDALG------ 348

Query: 344 DSRIELEMRTDHKELAEHLMLVDLARNDLARICQAGSRYVADLTKVDRYSFVMHLVSRVV 403
           D+    E+ +  KE +E  M  D+ RND +R+C+ GS  V    +++ YS ++H V  + 
Sbjct: 349 DAENIQELLSSVKEKSELTMCTDVDRNDKSRVCEPGSVRVIGRRQIEMYSRLIHTVDHIE 408

Query: 404 GTLRADLDVLHAYQACMNMGTLSGAPKVRAMQLIAALRSTRRGSYGG 450
           GTLR D D L A+   M   T++GAPK  AM+ I    ++ R  YGG
Sbjct: 409 GTLRRDFDALDAFLTHMWAVTVTGAPKTWAMRFIERHETSPRRWYGG 455


Lambda     K      H
   0.320    0.135    0.387 

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: 491
Number of extensions: 26
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: 519
Length of database: 457
Length adjustment: 34
Effective length of query: 485
Effective length of database: 423
Effective search space:   205155
Effective search space used:   205155
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: 52 (24.6 bits)

This GapMind analysis is from Apr 10 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:

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