GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Cereibacter sphaeroides ATCC 17029

Align Imidazole glycerol phosphate synthase subunit HisF; EC 4.3.2.10; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF (uncharacterized)
to candidate WP_009566362.1 RSPH17029_RS04675 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= curated2:A4YI34
         (251 letters)



>NCBI__GCF_000015985.1:WP_009566362.1
          Length = 239

 Score =  115 bits (289), Expect = 6e-31
 Identities = 73/237 (30%), Positives = 118/237 (49%), Gaps = 8/237 (3%)

Query: 10  LDVKDGKVVK---GVRFLDLKLKGDPAELASRYEEEGADEIVFLDISATVEGRKTLLEKV 66
           +D+KDG+ V+   G          DPA  A+ +E  G + +  +D++    GR      V
Sbjct: 7   IDLKDGQCVRLLRGEMEAATVFGDDPAAQAAAFEAAGCEWVHLVDLNGAFAGRPVNAAAV 66

Query: 67  RETASVLSIPLTVGGGVRTVEDVSNLLSNGADKVSLNTVAAENPSVVSMASREFGAQAVV 126
               + +++P  +GGG+R +  ++  L  G  +V L TVA ENP +V  A+R F  + V 
Sbjct: 67  EAILARIAVPAQLGGGIRDMATIALWLEKGLARVILGTVAVENPGLVREAARAFPGR-VA 125

Query: 127 VAIDAKRVGNGWRVFVRSGTKDTGLDAVDWAKRVEEMGAGEILLTSIDRDGTRDGYDLEL 186
           V IDA++     RV  +    +T + A D A+  E+ G   I+ T IDRDG   G ++E 
Sbjct: 126 VGIDARK----GRVATKGWATETDVMATDLARSFEDAGVAAIIYTDIDRDGAMAGPNIEA 181

Query: 187 TKAVVRATKVPVIASGGAGKPDHFLSVFRQAGADAALAAGIFHDGVIRIRELKDYLK 243
           T A+ RA  +PVIASGG       L++        A++    +DG + + +    L+
Sbjct: 182 TDALARAVSIPVIASGGVSSLADLLALRDTGSIAGAISGRALYDGALDLTQALQALR 238


Lambda     K      H
   0.317    0.135    0.374 

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: 129
Number of extensions: 6
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: 251
Length of database: 239
Length adjustment: 24
Effective length of query: 227
Effective length of database: 215
Effective search space:    48805
Effective search space used:    48805
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: 46 (22.3 bits)

This GapMind analysis is from Apr 16 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