GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisB in Pseudomonas fluorescens FW300-N1B4

Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate Pf1N1B4_1627 Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19)

Query= uniprot:Q9HU41
         (197 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1627
          Length = 211

 Score =  369 bits (946), Expect = e-107
 Identities = 179/197 (90%), Positives = 187/197 (94%)

Query: 1   MAERKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGD 60
           MAER ASV RDTLETQIK SI+LDGTGKARFD GVPFL+HM+DQIARHGLIDLDI  KGD
Sbjct: 15  MAERMASVERDTLETQIKASINLDGTGKARFDIGVPFLEHMLDQIARHGLIDLDIVSKGD 74

Query: 61  LHIDDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH 120
           LHIDDHHTVED+GITLGQAF KAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH
Sbjct: 75  LHIDDHHTVEDVGITLGQAFTKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH 134

Query: 121 VPFTRASVGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAI 180
           VP+TRA+VGGFDVDLF EFFQGFVNHA VTLHIDNLRGHNTHHQIETVFKAFGRALRMA+
Sbjct: 135 VPYTRATVGGFDVDLFQEFFQGFVNHANVTLHIDNLRGHNTHHQIETVFKAFGRALRMAV 194

Query: 181 ELDERMAGQMPSTKGCL 197
           ELD+RMAGQMPSTKG L
Sbjct: 195 ELDDRMAGQMPSTKGVL 211


Lambda     K      H
   0.325    0.141    0.421 

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: 279
Number of extensions: 8
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: 197
Length of database: 211
Length adjustment: 21
Effective length of query: 176
Effective length of database: 190
Effective search space:    33440
Effective search space used:    33440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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