GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Synechococcus elongatus PCC 7942

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate Synpcc7942_2582 Synpcc7942_2582 myo-inositol-1(or 4)-monophosphatase

Query= curated2:P56160
         (259 letters)



>FitnessBrowser__SynE:Synpcc7942_2582
          Length = 273

 Score = 99.8 bits (247), Expect = 5e-26
 Identities = 76/228 (33%), Positives = 112/228 (49%), Gaps = 10/228 (4%)

Query: 5   LQLALELAEKAGKLTLDYFGRRSLQVFSK-RDDTPVTEADRNAEELIRQGISAKFPDDGL 63
           L +A E A  AG   LD F  R  Q+  K R    +TEADR AE  +   +    PD  +
Sbjct: 13  LDVATEAALAAGA-ELDRFWGRLTQIEEKGRPGDLLTEADRAAEAAVLSVLERHCPDHAV 71

Query: 64  FGEEFDEHPSGNGRR---WIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALG 120
             EE     SG+ ++   W +DP+DGT ++ HG P  G  IAL  +    +GV   P L 
Sbjct: 72  LAEESGW--SGDRQQEFSWAVDPLDGTTNYAHGYPFCGTSIALLYQNQPIVGVFYAPYLK 129

Query: 121 ELYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLR---IDAGL 177
           EL++A +G GA +N  P++VS   + + S +V        +   N+  +  R   +  G+
Sbjct: 130 ELFRAAQGLGATLNRQPIRVSKTEKLAKSLLVTGFAYDRCEVEDNNYAEFCRLTHVTQGV 189

Query: 178 VRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDY 225
            RG         VA GR +   ++ +SPWD AA + +V+EAGG    Y
Sbjct: 190 RRGGSAALDLSYVACGRLDGYWERGLSPWDLAAGVVLVQEAGGLVTAY 237


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: 139
Number of extensions: 6
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: 273
Length adjustment: 25
Effective length of query: 234
Effective length of database: 248
Effective search space:    58032
Effective search space used:    58032
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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