GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Pseudomonas fluorescens FW300-N2E3

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate AO353_12070 AO353_12070 imidazoleglycerol-phosphate dehydratase

Query= SwissProt::D2QPE6
         (382 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12070
          Length = 197

 Score =  194 bits (493), Expect = 2e-54
 Identities = 96/194 (49%), Positives = 132/194 (68%), Gaps = 2/194 (1%)

Query: 191 RTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGDLHI 250
           R A VER+T ETQI+  +NLDG G+A  + G+ F +HMLDQ+A+H   DL I   GDLHI
Sbjct: 4   RKASVERDTLETQIKASINLDGTGKARFNIGVPFLEHMLDQIARHGLIDLDIECKGDLHI 63

Query: 251 DEHHTIEDTALALGEAYRRALGDKRGISRYGF-LLPMDEALAQVGIDFSGRPWLVWDAEF 309
           D+HHT+ED  + LG+A+ +A+GDK+GI RYG   +P+DEAL++V IDFSGRP L     +
Sbjct: 64  DDHHTVEDVGITLGQAFTKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMHVPY 123

Query: 310 KREKIGDMPTEMFYHFFKSFSDTALCNLNI-KVEGDNEHHKIEAIFKAFAKAIKMAVRRD 368
            R  +G    ++F  FF+ F + A  +L+I  + G N HH+IE +FKAF +A++MAV  D
Sbjct: 124 TRATVGGFDVDLFQEFFQGFVNHANVSLHIDNLRGHNTHHQIETVFKAFGRALRMAVELD 183

Query: 369 INELDNLPSTKGVL 382
                 +PSTKGVL
Sbjct: 184 ERMAGQMPSTKGVL 197


Lambda     K      H
   0.320    0.136    0.403 

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: 218
Number of extensions: 16
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: 382
Length of database: 197
Length adjustment: 25
Effective length of query: 357
Effective length of database: 172
Effective search space:    61404
Effective search space used:    61404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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