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_093427373.1 BM272_RS03710 3'(2'),5'-bisphosphate nucleotidase CysQ

Query= BRENDA::P95189
         (260 letters)



>NCBI__GCF_900112605.1:WP_093427373.1
          Length = 269

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 78/228 (34%), Positives = 108/228 (47%), Gaps = 12/228 (5%)

Query: 11  ALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFG 70
           A+A RA E     +   D  ++TK D +P+T+ADRA    + + L    P   VL EE G
Sbjct: 10  AIAHRAGEAILDVYHRADQGVETKADDSPLTEADRAAHRIIAEALAEAYPDIPVLSEE-G 68

Query: 71  GSTTFT-----GRQWIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWW 125
               +       R ++VDP+DGTK F+     +   IAL+E+G P  GVV APAL R  +
Sbjct: 69  AEIPYAERAHWSRLFVVDPLDGTKEFLHKNGEFTVNIALVEEGEPVAGVVHAPALGRT-Y 127

Query: 126 AARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRVR 185
              G GA +  DGARP  +++     +             A P ++     L +    + 
Sbjct: 128 LGDGNGA-SRRDGARP-PMAIRVADPVAGRPWRVVGSRSHATPEVQALVDALGEA--ELV 183

Query: 186 AYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRLTSLD 232
           + G  L  CLVAEGA D+       S WD AA   VVR AGG +   D
Sbjct: 184 SMGSSLKLCLVAEGAADLYPRLGPTSEWDTAAAHAVVRAAGGVVVDTD 231


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: 162
Number of extensions: 10
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: 260
Length of database: 269
Length adjustment: 25
Effective length of query: 235
Effective length of database: 244
Effective search space:    57340
Effective search space used:    57340
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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