GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisB in Azospirillum brasilense Sp245

Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate AZOBR_RS01665 AZOBR_RS01665 imidazoleglycerol-phosphate dehydratase

Query= uniprot:B2SZ63
         (195 letters)



>FitnessBrowser__azobra:AZOBR_RS01665
          Length = 207

 Score =  232 bits (592), Expect = 3e-66
 Identities = 112/195 (57%), Positives = 144/195 (73%)

Query: 1   MRLAEVVRNTSETQIRVKINLDGTGQQKLATGVPFLDHMLDQIARHGLFDLEIEAHGDLH 60
           +R A + RNT+ET+IRV +NLDGTG   + TGV FLDHML+Q++RH L DL + A GDLH
Sbjct: 9   VRRASIERNTTETRIRVAVNLDGTGVYDVKTGVGFLDHMLEQLSRHSLMDLTVAAEGDLH 68

Query: 61  IDDHHTVEDTGITLGQAVAKAIGDRKGIVRYGHSYVPLDEALSRVVIDFSGRPGLEFHVP 120
           ID HHT ED+GI +GQAVAKA+GDRKGI RYGH+Y+P+DE L+RV +DFS RP L + V 
Sbjct: 69  IDAHHTTEDSGIAIGQAVAKALGDRKGIQRYGHAYIPMDETLTRVALDFSNRPYLIWKVS 128

Query: 121 FTRARIGTFDVDLSIEFFRGFVNHAGVTLHIDNLRGLNAHHQMETVFKAFGRALRMATEL 180
           F+R +IG  D +L  E+F+ F   AGVTLH++ L G N HH +E+ +KA  RALR   E+
Sbjct: 129 FSRDKIGDMDTELFREWFQAFAMAAGVTLHVECLYGENNHHIVESCYKALARALRAGIEI 188

Query: 181 DERAAGQIPSTKGSL 195
           D R    +PSTKG+L
Sbjct: 189 DPRKRDAVPSTKGTL 203


Lambda     K      H
   0.323    0.140    0.408 

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: 160
Number of extensions: 5
Number of successful extensions: 1
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: 195
Length of database: 207
Length adjustment: 21
Effective length of query: 174
Effective length of database: 186
Effective search space:    32364
Effective search space used:    32364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 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