GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Pseudomonas putida KT2440

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate PP_0966 PP_0966 Histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__Putida:PP_0966
          Length = 441

 Score =  248 bits (632), Expect = 7e-70
 Identities = 143/402 (35%), Positives = 230/402 (57%), Gaps = 13/402 (3%)

Query: 391 IIENVRDKGNSALLEYTEKFDGV---KLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENV 447
           II+ VR++G++AL+E+T++FDGV    + + +L+    E     +T   +EAL+ +   V
Sbjct: 42  IIKAVRERGDAALVEFTQRFDGVDAKSIDDLILDRARLELALTRITPVQREALEKAANRV 101

Query: 448 RKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQC 507
           R +H  Q   ++ +     G +  +   P+++ GLY+PGG A  PS+ LM  +PA+VA  
Sbjct: 102 RIYHERQ-KQDSWQYTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGV 160

Query: 508 KEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGP 567
            E+V   P  +  G+V+  V+  A   G  ++   GGAQAVAA+AYGTE++P+VDKI+GP
Sbjct: 161 TEVVMVVPTPR--GEVNELVLAAACIAGVDRVFTVGGAQAVAALAYGTESVPQVDKIVGP 218

Query: 568 GNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQV 627
           GN +V  AK +V         IDM AGPSE+LV+ D   D D++A DL SQAEH  D+Q 
Sbjct: 219 GNIYVATAKRHVFGQV----GIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQA 274

Query: 628 ILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAP 686
           ILV  + +   +  +  ++      + R DI+ K I     ++     ++A++++N+ AP
Sbjct: 275 ILVSPDAAF--LDRVAASIDKLMPTMERADIIEKSINGRGALIQVRDMQQAMDVANRIAP 332

Query: 687 EHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTAT 746
           EHL L +A+   ++  + +AG++F+G +T E+ GDY +G NH LPT G AR  S      
Sbjct: 333 EHLELSVADPQAWLPHIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVYD 392

Query: 747 FQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788
           FQK  +    + +G   +G     +A+ E L  H  + + R+
Sbjct: 393 FQKRSSIIFCSEQGASELGHTASVLARGESLTAHARSAEYRI 434


Lambda     K      H
   0.315    0.133    0.371 

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: 694
Number of extensions: 40
Number of successful extensions: 5
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: 799
Length of database: 441
Length adjustment: 37
Effective length of query: 762
Effective length of database: 404
Effective search space:   307848
Effective search space used:   307848
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: 42 (22.0 bits)
S2: 53 (25.0 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