Alignments for a candidate for hisE in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisE in Pseudomonas fluorescens FW300-N2E2

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Pf6N2E2_3252 Histidinol dehydrogenase (EC 1.1.1.23)

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252
          Length = 445

 Score =  249 bits (635), Expect = 3e-70
 Identities = 144/403 (35%), Positives = 232/403 (57%), Gaps = 15/403 (3%)

Query: 391 IIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFE----GLTEEMKEALDLSIEN 446
           II+ VR++G++AL+E+T+KFDG+++++ + +   P E  E     +T   +EAL+ +   
Sbjct: 42  IIKAVRERGDAALVEFTQKFDGLQVAS-MADLILPRERLELALTRITVPQREALEKAASR 100

Query: 447 VRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQ 506
           VR +H  Q        E    VL  +   P+++ GLY+PGG A  PS+ LM  +PA+VA 
Sbjct: 101 VRDYHERQKQDSWSYTEADGTVLGQKVT-PLDRAGLYVPGGKASYPSSVLMNAIPAKVAG 159

Query: 507 CKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILG 566
             E+V   P  +  G+++  V+  A   G  ++   GGAQAVAA+AYGTE++P+VDK++G
Sbjct: 160 VTEVVMVVPTPR--GEINELVLAAACIAGVDRVFTIGGAQAVAALAYGTESVPRVDKVVG 217

Query: 567 PGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQ 626
           PGN +V  AK +V         IDM AGPSE+LV+ D   D D++A DL SQAEH  D+Q
Sbjct: 218 PGNIYVATAKRHVFGQV----GIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQ 273

Query: 627 VILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYA 685
            ILV  +   + + ++  ++      + R +I+   I     ++     E+A+E++N+ A
Sbjct: 274 AILVSPDA--EFLDKVAASIDKLLPTMDRAEIINTSINGRGALIHVRDMEQAIEVANRIA 331

Query: 686 PEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTA 745
           PEHL L +A+   ++  + +AG++F+G +T E+ GDY +G NH LPT G AR  S     
Sbjct: 332 PEHLELSVADPQAWLPQIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVY 391

Query: 746 TFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788
            FQK  +    + +G   +G+    +A+ E L  H  + + R+
Sbjct: 392 DFQKRSSIIFCSEQGASELGKTASVLARGESLSAHARSAEYRI 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: 729
Number of extensions: 33
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: 445
Length adjustment: 37
Effective length of query: 762
Effective length of database: 408
Effective search space:   310896
Effective search space used:   310896
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis