GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Shewanella loihica PV-4

Align histidinol-phosphatase (EC 3.1.3.15); inositol-phosphate phosphatase (EC 3.1.3.25) (characterized)
to candidate 5209868 Shew_2321 inositol monophosphatase (RefSeq)

Query= BRENDA::Q6NPM8
         (346 letters)



>FitnessBrowser__PV4:5209868
          Length = 267

 Score =  110 bits (276), Expect = 3e-29
 Identities = 71/225 (31%), Positives = 115/225 (51%), Gaps = 13/225 (5%)

Query: 94  ADASGEVIRKYFRK--KFDIVDKDDMSPVTIADQMAEEAMVSIIFQNLPSHAIYGEEKGW 151
           A A+G+ I + + +  + ++  K     VT  D+ AE A+   I ++ P H I GEE G 
Sbjct: 12  ARAAGQTIMRAYTELDRVEVSAKGINDYVTNVDKEAEAAITYQIRKSYPDHTIVGEENGE 71

Query: 152 RCKEESADYVWVLDPIDGTKSFITGKPVFGTLIALLYKGKPILGLIDQPILKERWIGMNG 211
             K +++DY+W++DP+DGT +F+ G P F   IA+ +KGK  + ++  P+  E +  + G
Sbjct: 72  N-KGQNSDYMWIVDPLDGTNNFVRGIPHFAVSIAVQHKGKTEVAVVYDPVRDELFTAVRG 130

Query: 212 RRTKLNGEDISTRSCPKLSQAYLYTTSPHLFSEEAE-------KAYSRVRDKVKVPLYGC 264
           +  KLN   I       L +A + T  P    +  E         +S+  D  +    G 
Sbjct: 131 KGAKLNDFRIRVSKASDLDEAIVGTGFPFKAKQHTETYMKLFASTFSQCADLRRA---GS 187

Query: 265 DCYAYALLASGFVDLVIESGLKPYDFLALVPVIEGAGGTITDWTG 309
                A +A+G +D   E GLKP+D  A   ++  AGGT+TD+TG
Sbjct: 188 AALDLAYVAAGRMDAFFEIGLKPWDIAAGDLIVREAGGTVTDFTG 232


Lambda     K      H
   0.318    0.133    0.392 

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: 174
Number of extensions: 8
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: 346
Length of database: 267
Length adjustment: 27
Effective length of query: 319
Effective length of database: 240
Effective search space:    76560
Effective search space used:    76560
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 (21.7 bits)
S2: 48 (23.1 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