GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Pseudomonas fluorescens FW300-N2E3

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate AO353_15815 AO353_15815 inositol monophosphatase

Query= reanno::azobra:AZOBR_RS03845
         (260 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15815
          Length = 272

 Score = 99.4 bits (246), Expect = 7e-26
 Identities = 85/263 (32%), Positives = 124/263 (47%), Gaps = 15/263 (5%)

Query: 8   PLVTLAERLA-DASGPVIRQYFRTP-VAVDDKADASPVTIADREAERTIRAIIEAERPDD 65
           P++ +A R A  AS  + R   R   + VD+K     V+  DR AE+ I   +    P+ 
Sbjct: 3   PMLNIALRAARSASELIFRSIERLDTIKVDEKDAKDYVSEVDRAAEQKIIDALRKAYPNH 62

Query: 66  GIYGEEFGTKNLDA----EWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQP 121
            I GEE G    +     E++W+IDP+DGT +F+ G P F   IA  +RGR    V+  P
Sbjct: 63  SIMGEETGMHAGNGIEGEEYLWIIDPLDGTTNFLRGIPHFAVSIACKYRGRLEHAVVLDP 122

Query: 122 IVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSP---DLFPGADQ--DAFRRVA 176
           + ++ +    GR    NG+  RV      L  A LGT  P   D     D     FR + 
Sbjct: 123 VRQEEFTASRGRGAQLNGRRLRV-SGRTSLDGALLGTGFPFRDDQMDNLDNYLGMFRALV 181

Query: 177 G-AAKVSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLD 235
           G  A +   G        +AAG +D   ESGL  +D AA   ++  AGGL++D+ G   D
Sbjct: 182 GQTAGIRRAGAASLDLAYVAAGRFDAFWESGLSEWDMAAGALLIQEAGGLVSDFTGGH-D 240

Query: 236 ATSSGRVVAAGDARTHRETLAAL 258
               G +V AG+ +  +  L A+
Sbjct: 241 FLEKGHIV-AGNTKCFKAVLTAI 262


Lambda     K      H
   0.320    0.139    0.424 

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: 153
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: 260
Length of database: 272
Length adjustment: 25
Effective length of query: 235
Effective length of database: 247
Effective search space:    58045
Effective search space used:    58045
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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