GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Trichormus variabilis ATCC 29413

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_011317835.1 AVA_RS04970 inositol monophosphatase family protein

Query= curated2:P56160
         (259 letters)



>NCBI__GCF_000204075.1:WP_011317835.1
          Length = 270

 Score = 99.4 bits (246), Expect = 7e-26
 Identities = 76/253 (30%), Positives = 119/253 (47%), Gaps = 5/253 (1%)

Query: 5   LQLALELAEKAGKLTLDYFGRRSLQVFSK-RDDTPVTEADRNAEELIRQGISAKFPDDGL 63
           L +A E A  AG +   Y G+    V  K R    VT AD+ +E ++ + I   FP   +
Sbjct: 8   LDIATEAALAAGAVLQGYLGKLEDAVTEKGRPGDLVTAADKASEAVVLEIIRRHFPQHSI 67

Query: 64  FGEEFDEHPS-GNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGEL 122
             EE  +  +  N   W IDP+DGT ++ H  P + V I L + G  Q+GVI  P   EL
Sbjct: 68  LAEESGKLGNQDNEYLWAIDPLDGTTNYAHQYPAFCVSIGLLINGVPQVGVIYDPFHDEL 127

Query: 123 YQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVD---QLRIDAGLVR 179
           ++   G GA  +  P++VS  +E S S +V        + P N+  +      +  G+ R
Sbjct: 128 FRGAAGLGATRDRRPIKVSDTSELSKSLLVTGFAYDRRETPDNNYAEFCHLTHLTQGVRR 187

Query: 180 GWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVS 239
                     VA GR +   ++ +SPWD  A + +++EAGG    Y G    I    +++
Sbjct: 188 SGSAALDLAHVACGRVDGYWERGISPWDIVAGVILLQEAGGKVTAYDGTPLKIATGRILA 247

Query: 240 ANNAMGRNLIAAI 252
            N ++  NL  A+
Sbjct: 248 TNGSIHDNLSRAL 260


Lambda     K      H
   0.319    0.138    0.415 

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: 157
Number of extensions: 7
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: 259
Length of database: 270
Length adjustment: 25
Effective length of query: 234
Effective length of database: 245
Effective search space:    57330
Effective search space used:    57330
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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