GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Thiohalospira halophila DSM 15071 HL 3

Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_093427934.1 BM272_RS06385 inositol monophosphatase

Query= BRENDA::Q8NS80
         (260 letters)



>NCBI__GCF_900112605.1:WP_093427934.1
          Length = 275

 Score = 85.1 bits (209), Expect = 1e-21
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 27/242 (11%)

Query: 6   DDLALALELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADS 65
           D  A+A  +   A++  L R+E    E   K D + V++AD A +EAL  ++A   PA  
Sbjct: 8   DLAAVAACVRRAAEAELLPRYERVGHEF--KADGSLVTEADTACQEALTAELARLAPAIP 65

Query: 66  ILGEEFGGDVE---FSGRQ---WIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISA 119
           +LGEE     +    +G +   WI+DP+DGT N+  G+P ++  +AL+  G+    V+  
Sbjct: 66  LLGEEMTAAEQADYLTGNEAGLWILDPLDGTGNFAVGIPFFSISLALVVAGRVELAVVYH 125

Query: 120 PALARRWWASEGAGAW----RTFNGSSPRKLSVSQVSKLDDASLSFSSLSGWAERDLRDQ 175
           P     + A+ G GAW    R   G  P    ++  S L D     + L+          
Sbjct: 126 PTTGECFTAARGEGAWLDGERLGEGFQP---DLAHASALVDFKRLPTGLAA--------- 173

Query: 176 FVSLTDTTWR-LRGYGDF-FSYCLVAEGAVDIAAEPEVSLWDLAPLSILVTEAGGKFTSL 233
               T+  +R  R +G     +C VA G   +       +WDLA  S++++EAGG   +L
Sbjct: 174 -ALATEPPYRSQRSFGSVALDWCWVAAGRCHLYVHGGQKVWDLAAGSLILSEAGGHAATL 232

Query: 234 AG 235
           AG
Sbjct: 233 AG 234


Lambda     K      H
   0.315    0.133    0.396 

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: 210
Number of extensions: 11
Number of successful extensions: 3
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: 275
Length adjustment: 25
Effective length of query: 235
Effective length of database: 250
Effective search space:    58750
Effective search space used:    58750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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