GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Paraburkholderia bryophila 376MFSha3.1

Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate H281DRAFT_00539 H281DRAFT_00539 myo-inositol-1(or 4)-monophosphatase

Query= SwissProt::P95189
         (260 letters)



>FitnessBrowser__Burk376:H281DRAFT_00539
          Length = 267

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 81/262 (30%), Positives = 124/262 (47%), Gaps = 12/262 (4%)

Query: 3   HDDLMLALALADRADELTRVRFGALDL-RIDTKPDLTPVTDADRAVESDVRQTLGRDRPG 61
           H  L +A+  A RA ++       LDL ++  K     VT+ D+A E+ +  TL    P 
Sbjct: 2   HPMLNIAVKAARRAAQIINRASLDLDLIQVSKKQHNDFVTEIDKASEAAIIDTLKTAYPD 61

Query: 62  DGVLGEEFGGSTTFTGRQWIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQ 121
             +L EE G S   +  QWI+DP+DGT NF+ G P +   IAL   G+ +  VV  P   
Sbjct: 62  HAILAEESGKSDNESEYQWIIDPLDGTTNFIHGFPYYCVSIALAHKGIVTQAVVYDPTRN 121

Query: 122 RRWWAARGRGAFAS---VDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLT 178
             + A+RGRGAF +   +  A+  RL+      L      F    G    G   +F  +T
Sbjct: 122 DLFTASRGRGAFLNDRRIRVAKRDRLADG----LIGTGFPFRETDGLEAYG--RQFAEMT 175

Query: 179 DTVWRVRAYG-DFLSYCLVAEGAVDIAAEPQVSVWDLAALDIVVREAGGRLTSLDGVAG- 236
                +R  G   L    VA G +D   E  ++ WD+AA  +++ EAGG + +  G +  
Sbjct: 176 QACAGLRRPGAAALDLANVAAGRMDGFFEQGLNPWDVAAGSLLITEAGGLVGNYTGDSEF 235

Query: 237 PHGGSAVATNGLLHDEVLTRLN 258
            H G  VA N  ++ +++  L+
Sbjct: 236 LHVGEIVAGNPKIYAQMVPILS 257


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: 160
Number of extensions: 7
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: 267
Length adjustment: 25
Effective length of query: 235
Effective length of database: 242
Effective search space:    56870
Effective search space used:    56870
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