GapMind for Amino acid biosynthesis

 

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

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Pf6N2E2_2862 Uncharacterized PLP-dependent aminotransferase YfdZ

Query= curated2:Q3A7R3
         (347 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2862
          Length = 405

 Score = 77.8 bits (190), Expect = 5e-19
 Identities = 73/241 (30%), Positives = 115/241 (47%), Gaps = 19/241 (7%)

Query: 76  DPDW-VIMANGSDEVLNNLIRAFAGEGEEIAYVHPSYSYYSTLAEIQGAKVRTFLLDEGW 134
           DP+   I+  GS E L +L+ A   +G+ +   +PSY  +   A I GA+VR+  L  G 
Sbjct: 96  DPETEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPSYPIHIYGAVIAGAQVRSVPLVPGV 155

Query: 135 ALKDFPERYTG------KLFFLTNPNAPLGFCYPQEFIEE---LAGRVDGMLVVDEAYAD 185
                 ER         K+  L  P+ P   C   +F E    LA + D +++ D AYAD
Sbjct: 156 DFFAELERAIRGSIPKPKMMILGFPSNPTAQCVELDFFERVIALAKQYDVLVIHDLAYAD 215

Query: 186 FA----KENSLDLVRRLPNVVVTR-TFSKSYSLAGMRLGLAIAHPEVIAALNKIRDHYNL 240
                 K  S+  V    ++ V   T SKSY++AG R+G  + +PE++ AL +I+ +++ 
Sbjct: 216 IVYDGWKAPSIMQVPGAKDIAVEFFTLSKSYNMAGWRIGFMVGNPELVNALARIKSYHDY 275

Query: 241 DRLA--QTACVAAL-ADQEYFQQCVSKIRETRDWFSAELRVLDWDV-IPSHGNFVFATPP 296
                 Q A +AAL  DQ+  +    + R+ R+     L  L W V  P    +V+A  P
Sbjct: 276 GTFTPLQVAAIAALEGDQQCVRDIAEQYRQRRNVLVKGLHELGWMVENPKASMYVWAKIP 335

Query: 297 D 297
           +
Sbjct: 336 E 336


Lambda     K      H
   0.320    0.137    0.413 

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: 380
Number of extensions: 19
Number of successful extensions: 4
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: 347
Length of database: 405
Length adjustment: 30
Effective length of query: 317
Effective length of database: 375
Effective search space:   118875
Effective search space used:   118875
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: 50 (23.9 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