GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Synechococcus elongatus PCC 7942

Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate Synpcc7942_1763 Synpcc7942_1763 inositol monophosphate family protein

Query= SwissProt::P95189
         (260 letters)



>FitnessBrowser__SynE:Synpcc7942_1763
          Length = 272

 Score = 78.2 bits (191), Expect = 2e-19
 Identities = 70/238 (29%), Positives = 103/238 (43%), Gaps = 26/238 (10%)

Query: 11  ALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFG 70
           AL     +   + FG L  +   K D + +T ADR  +  +   L +  P   +L EE  
Sbjct: 15  ALCQEVGDRLLLEFGTL--QATEKADGSLITAADRWADQTLCDRLSQLFPKHALLTEE-- 70

Query: 71  GSTTFTGRQW--IVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAAR 128
              TF G  W  +VDP+DGT NF +G+P+W   +ALL  G P  G ++ P LQR +    
Sbjct: 71  SQQTFGGADWTWVVDPLDGTTNFAQGIPIWGISLALLYRGWPVFGAIALPPLQRFYCGVD 130

Query: 129 GRGA-FASVDGA----RPHRLSVSSVAELHSASLSFSS---LSGWARP-GLRERFIGLTD 179
            R    A V  A    +P +L   S+      SL   S   L  W+ P   + R +G + 
Sbjct: 131 TRSTDLAPVAWAERNHQPLQLRTESLGSNQLFSLCTRSAIVLQRWSAPFPCKIRMLGAST 190

Query: 180 TVWRVRAYGDFLSYCLVAEGAVDIAAEPQVSVWDLAALDIVVREAGGRLTSLDGVAGP 237
                       ++  V EG    A E    +WD+AA+ ++ +  G    SL G   P
Sbjct: 191 A-----------NFLTVLEGTTLGALEATPKIWDIAAVWVLAQALGADWRSLAGEQFP 237


Lambda     K      H
   0.319    0.136    0.414 

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: 179
Number of extensions: 9
Number of successful extensions: 2
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: 260
Length of database: 272
Length adjustment: 25
Effective length of query: 235
Effective length of database: 247
Effective search space:    58045
Effective search space used:    58045
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