GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Pseudomonas stutzeri RCH2

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate GFF1214 Psest_1247 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family

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



>FitnessBrowser__psRCH2:GFF1214
          Length = 271

 Score =  103 bits (257), Expect = 4e-27
 Identities = 82/264 (31%), Positives = 130/264 (49%), Gaps = 18/264 (6%)

Query: 8   PLVTLAERLADASGP-VIRQYFRTP-VAVDDKADASPVTIADREAERTIRAIIEAERPDD 65
           P++ +A R A ++G  ++R   R   ++V++K     VT  D+ AE++I A +    P+ 
Sbjct: 3   PMLNIALRAARSAGELIVRSTDRLDAISVNEKEAKDYVTEIDKAAEQSIVAALRKAYPNH 62

Query: 66  GIYGEEFGT---KNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPI 122
           GI GEE G         +++W+IDP+DGT +F+ G P +   IA  +RGR    V+  P+
Sbjct: 63  GILGEEGGLLEGSGDGTDYLWIIDPLDGTTNFVRGIPHYAVSIACKYRGRLEHAVVLDPV 122

Query: 123 VRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQD-------AFRRV 175
            ++ +    GR    NG+  RV      L  A LGT  P  F   D D        FR +
Sbjct: 123 RQEEFTASRGRGAAVNGRRLRV-SARKSLDGALLGTGFP--FKDGDMDNLDAYLNMFRSL 179

Query: 176 AG-AAKVSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPL 234
            G  + +   G        +AAG +D   E GL  +D AA   ++  AGGL++D+ G   
Sbjct: 180 VGQTSGLRRAGAASLDLAYVAAGRFDAFWEFGLSEWDMAAGALLIQEAGGLVSDFSGGH- 238

Query: 235 DATSSGRVVAAGDARTHRETLAAL 258
           D    G++V AG+ +  +  L A+
Sbjct: 239 DFLEKGQIV-AGNTKCFKAVLTAI 261


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: 173
Number of extensions: 5
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: 260
Length of database: 271
Length adjustment: 25
Effective length of query: 235
Effective length of database: 246
Effective search space:    57810
Effective search space used:    57810
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.

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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