GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Caldicellulosiruptor kronotskyensis 2002

Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_013429993.1 CALKRO_RS05030 histidinol-phosphatase HisJ family protein

Query= BRENDA::Q02150
         (269 letters)



>NCBI__GCF_000166775.1:WP_013429993.1
          Length = 266

 Score =  151 bits (381), Expect = 2e-41
 Identities = 89/262 (33%), Positives = 142/262 (54%), Gaps = 11/262 (4%)

Query: 5   DYHFHSHFSADSEELPRKHVTEAIAHGLEEICFTEHRDFYFPGMDF---SLNLPEYFQEI 61
           DYH HS+FS+DS       V +AI   LEEI FT+H D  +P + +    +N  +Y  E 
Sbjct: 3   DYHIHSNFSSDSNMNMEDAVKKAIELNLEEIAFTDHMDLLYPPVSYPVWDINYEDYMNEF 62

Query: 62  NRLQAEFKDKIKIKIGLEMGIDLRFKSEINQFIDSAPFDFVIASVHEIGDIEVYDGTEFY 121
             ++ ++  KIKIK+G E+G+      +  + ++S  FDFVIAS H +   ++ DG  FY
Sbjct: 63  YAIKKKYSSKIKIKLGSEVGLQPHSIEKSLEILNSYSFDFVIASTHVVDFQDLADGV-FY 121

Query: 122 LQKIKEEAQREYLLACLDVVQNFENYNSFGHLDYVARYGPYTDKSIKFAENREILFEILR 181
             K K++A   Y    L+++++F+ +  +GHLD V RYG Y +K +   E  +++ EIL+
Sbjct: 122 QGKTKQQAYIRYFEETLNLIKSFDKFCVYGHLDIVKRYGDYENKDLDKEEYWDLIDEILK 181

Query: 182 ALASKEKALEINTRLF----DDPKTEQFYSDLLINFKKLGGKFITLGTDSHIAKRDWLSI 237
            L  K K +E+NT  F      P  E     ++  F +LGG+ ITLG+D+H  +      
Sbjct: 182 LLIFKGKGIEVNTSGFRYGLGMPHPEY---KIIKRFYELGGEIITLGSDAHSTEYIAYMF 238

Query: 238 HKARTLIKKAGFHELATFSGMK 259
           +    ++K  GF  L  F  ++
Sbjct: 239 NYTVDMLKSIGFKYLTKFENLE 260


Lambda     K      H
   0.322    0.139    0.404 

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: 271
Number of extensions: 19
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: 269
Length of database: 266
Length adjustment: 25
Effective length of query: 244
Effective length of database: 241
Effective search space:    58804
Effective search space used:    58804
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 26 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