GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Desulfovibrio vulgaris Hildenborough

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 206472 DVU1038 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

Query= BRENDA::P16250
         (240 letters)



>MicrobesOnline__882:206472
          Length = 249

 Score =  166 bits (419), Expect = 5e-46
 Identities = 96/236 (40%), Positives = 137/236 (58%), Gaps = 4/236 (1%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           + PA+D+ +G  VRL  G +  ET + S P+  A  WQ  G  WLH+VDLD AF G   N
Sbjct: 3   VFPAIDLMNGVCVRLRRGRADDETVFSSDPVATARHWQEQGGRWLHVVDLDGAFSGQPVN 62

Query: 64  RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123
             LI  +  A+DI V+L GGIRD  T  A L  G  R+ +GT ALE P+  A + AE   
Sbjct: 63  APLIRSICDALDIPVQLGGGIRDAATAKAYLEAGVERLIIGTIALEEPDAYAALCAEFPG 122

Query: 124 KIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELL 182
           +I V LD  G  L+ +GW  D G  + E L RL + G A  + TDI +DG   G NL  L
Sbjct: 123 RIGVSLDAEGGKLKTKGWVADSGLTVDEVLPRLLEAGTAFIIYTDIDRDGMQTGVNLPAL 182

Query: 183 KNVCAATDRPVVASGGVSSLDDLRAIAGLV-PAGVEGAIVGKALYAKAFTLEEALE 237
           +++  A+  PV+A+GGV++L+D++A+  L     ++GA+ G+A+Y     L  A++
Sbjct: 183 EHLAKASTVPVIAAGGVATLEDVKALYPLSRTTNLQGAVSGRAIYEGTLDLRTAMD 238


Lambda     K      H
   0.315    0.133    0.385 

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: 176
Number of extensions: 16
Number of successful extensions: 6
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: 240
Length of database: 249
Length adjustment: 24
Effective length of query: 216
Effective length of database: 225
Effective search space:    48600
Effective search space used:    48600
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: 42 (22.0 bits)
S2: 46 (22.3 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:

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