GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Dyella japonica UNC79MFTsu3.2

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate N515DRAFT_1749 N515DRAFT_1749 histidinol-phosphatase

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



>FitnessBrowser__Dyella79:N515DRAFT_1749
          Length = 262

 Score =  167 bits (422), Expect = 3e-46
 Identities = 106/260 (40%), Positives = 142/260 (54%), Gaps = 12/260 (4%)

Query: 1   MTEPCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEA 60
           M+ P     ++ A   A+A+  VIR Y+R  V V+ K+DA+PVTIADREAE  IR +++A
Sbjct: 1   MSAPDLQRALSAAREAAEAAAEVIRHYWRRGVEVEIKSDATPVTIADREAELAIRKVLQA 60

Query: 61  ERPDDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQ 120
             P+  IYGEEFG  +   E +W++DP+DGTKSF+   P F T IAL+H+G  VLGV   
Sbjct: 61  ALPEAAIYGEEFGLDDGARELLWLVDPLDGTKSFVRRTPFFSTQIALMHKGELVLGVSSA 120

Query: 121 PIVRDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAA- 179
           P+  +      G    F G   RV      +A A++ T +         DA     GA  
Sbjct: 121 PVYGETLWASAGGGAWFEGDRVRV-AATDSMAQASISTGNVKTL---TMDARWAELGAMI 176

Query: 180 ----KVSVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLD 235
               ++  YG  C+ Y LLA G  DLV+ES + + D AAL  +V  AGGL TD DG+PL 
Sbjct: 177 RDSNRIRGYGDFCH-YHLLARGGLDLVIESDVNILDVAALAAIVREAGGLFTDLDGQPL- 234

Query: 236 ATSSGRVVAAGDARTHRETL 255
            T   R V AG    H + L
Sbjct: 235 -TLDTRSVLAGTPALHAQAL 253


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: 211
Number of extensions: 11
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: 262
Length adjustment: 25
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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