GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Bacteroides thetaiotaomicron VPI-5482

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate 352328 BT2801 inositol-1-monophosphatase (NCBI ptt file)

Query= curated2:P56160
         (259 letters)



>FitnessBrowser__Btheta:352328
          Length = 267

 Score = 99.4 bits (246), Expect = 7e-26
 Identities = 70/224 (31%), Positives = 105/224 (46%), Gaps = 13/224 (5%)

Query: 26  RSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLFGEEFDEHPSGNGRRWIIDPID 85
           R  +V  K     V+  D+ +E  + + +SA  P+ G   EE           W+IDP+D
Sbjct: 30  RRERVMEKHAHDYVSYVDKESEVRLVKALSALLPEAGFITEEGSATYQDEPYCWVIDPLD 89

Query: 86  GTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELYQAERGSGAFMNGSPVQVSAIAE 145
           GT ++IH    Y V IAL     + LGV+      E + A +G  AFMNG  + VS +  
Sbjct: 90  GTTNYIHDEAPYCVCIALRSRTELLLGVVYEVCRNECFYAWKGGKAFMNGEEIHVSDV-R 148

Query: 146 NSASTVVFTEKEYLLD---PPSNHPVDQLRIDAGLVRGWGD-----CYGHMLVASGRAEV 197
           +  +  VFTE  Y  D   P + H +D L    G +R  G      CY    +A+GR + 
Sbjct: 149 DIKNAFVFTELPYNYDQYKPTALHLIDNLYGAVGGIRMNGSAAAAICY----IANGRFDA 204

Query: 198 AVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVSAN 241
             +  +  WD +A   IV EAGG   ++ G    I+G  +++ N
Sbjct: 205 WAEAFIGKWDYSAAALIVLEAGGRVTNFYGDDHFIEGHHIIATN 248


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: 161
Number of extensions: 12
Number of successful extensions: 2
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: 267
Length adjustment: 25
Effective length of query: 234
Effective length of database: 242
Effective search space:    56628
Effective search space used:    56628
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