GapMind for Amino acid biosynthesis

 

Aligments for a candidate for IGPS in Desulfovibrio vulgaris Hildenborough

Align Indole-3-glycerol-phosphate synthase; EC 4.1.1.48 (characterized, see rationale)
to candidate 209404 DVU0468 indole-3-glycerol phosphate synthase

Query= uniprot:B8DM44_DESVM
         (321 letters)



>lcl|MicrobesOnline__882:209404 DVU0468 indole-3-glycerol phosphate
           synthase
          Length = 257

 Score =  305 bits (780), Expect = 1e-87
 Identities = 173/269 (64%), Positives = 196/269 (72%), Gaps = 14/269 (5%)

Query: 1   MLDRFRIAKQPELDRLRKLAEAGGMPAPLASGTGGGTPRPDFLRALRDRTGYPDAPVAVI 60
           ML+RFR AK+ E+D+L + A  GG+PAP A       PRP F  ALR         +AVI
Sbjct: 1   MLERFRAAKRHEVDKLEQCARRGGLPAPFAG------PRPAFGTALRGDG------LAVI 48

Query: 61  AEYKRASPSRGVIETGVSPEDAATAYATAGATAISVLTEEQYFGGDLTYLGRMAGVNPDV 120
           AEYKRASPS GVI+T ++PE+ ATAY   GATAISVLTEE +F G+L+YLGRM    P +
Sbjct: 49  AEYKRASPSCGVIDTKLTPEEVATAYEAGGATAISVLTEEVHFRGELSYLGRMTA--PGL 106

Query: 121 PLLRKDFIMDSLQVAATAATPAAALLLIVRLTPDAHTLRDLREQAETHGMHAVVEIFDEA 180
           PLLRKDFIM  LQV ATAATPA+ALLLIVRLTPDA  LRDLREQAE  GM AVVE+FD  
Sbjct: 107 PLLRKDFIMHPLQVTATAATPASALLLIVRLTPDAALLRDLREQAEAQGMDAVVEVFDTD 166

Query: 181 DLALARESGARIIQVNNRDLETLAVDRTACLRLGPLRAPGEVWIAASGISENRHLAEAAA 240
           DL +AR SGARIIQVN RDL+TL V   ACL +G LR   E W+AASG+S   HLA AA 
Sbjct: 167 DLDIARASGARIIQVNARDLDTLKVSMPACLGMGVLRDAAETWVAASGMSAPEHLAAAAT 226

Query: 241 AGYDAALVGTALMDGGDLKGSLMRLLGRE 269
           AGYDAALVGTALM GGD   +L  LLGRE
Sbjct: 227 AGYDAALVGTALMRGGDPGAALRALLGRE 255


Lambda     K      H
   0.316    0.133    0.386 

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: 275
Number of extensions: 13
Number of successful extensions: 3
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: 321
Length of database: 257
Length adjustment: 26
Effective length of query: 295
Effective length of database: 231
Effective search space:    68145
Effective search space used:    68145
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 (21.6 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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