GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Azospirillum brasilense Sp245

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate AZOBR_RS01680 AZOBR_RS01680 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= BRENDA::P16250
         (240 letters)



>FitnessBrowser__azobra:AZOBR_RS01680
          Length = 249

 Score =  152 bits (384), Expect = 6e-42
 Identities = 94/240 (39%), Positives = 130/240 (54%), Gaps = 7/240 (2%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           + PA+D++DG  VRL+ GE    T + + P + A  ++  G EWLHLVDL+ AF G   N
Sbjct: 3   IYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKPVN 62

Query: 64  RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123
              +  +  A+ I V+L GGIRD  T+A  L  G +RV LGT AL  PE V +   E   
Sbjct: 63  GKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREFPG 122

Query: 124 KIAVGLDVRGTTLRGRGWTRDGGDLYETLD---RLNKEGCARYVVTDIAKDGTLQGPNLE 180
           K+AVG+D R   +   GW        + LD   +    G A  + TDI +DG + G N+E
Sbjct: 123 KVAVGIDAREGYVAVAGWAETS--TIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180

Query: 181 LLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYAKAFTLEEALEATS 240
              ++      PV+ASGGVSS+DDL A+      G+EG I G+ALY      + AL+  S
Sbjct: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDLLS 240


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: 155
Number of extensions: 11
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: 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 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