GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Pseudomonas fluorescens FW300-N2C3

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate AO356_06375 AO356_06375 homoserine dehydrogenase

Query= uniprot:A0A1L6J6Q3
         (430 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_06375
          Length = 434

 Score =  337 bits (863), Expect = 6e-97
 Identities = 193/427 (45%), Positives = 268/427 (62%), Gaps = 16/427 (3%)

Query: 4   PLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARD---RAKDRGVDITRFD 60
           P++V + GLGTVG G   ++  NAE I+RRAGR IE+  ++ R    + +  G+ IT   
Sbjct: 3   PVKVGICGLGTVGGGTFNVLQRNAEEISRRAGRGIEVAQIAMRTPKPQFQTTGIAIT--- 59

Query: 61  WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120
             +D+ E+A +P+ D+V+EL+GG    A  L    +  GK +VTANKA+IA HG E+   
Sbjct: 60  --NDVFEVATNPEIDIVIELVGGYT-VARELVLKAIENGKHVVTANKALIAVHGNEIFAK 116

Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180
           A +    + FEAAVAGG+PVIK +REG +AN+I+ V GI+NGT NFIL++M  +GR F +
Sbjct: 117 AREKGVIVAFEAAVAGGIPVIKAIREGLSANRINWVAGIINGTGNFILTEMREKGRTFED 176

Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240
           VLAEAQA G+AEADP+FD++G+DAAHKL+ILASIAFG    F      GI  L  AD+  
Sbjct: 177 VLAEAQALGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKAYTEGITQLTTADVNY 236

Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300
           A ALGYRI+ LG+A  + +G+  RVHP L+P    +A+V G  NAV+  G+  G  LF G
Sbjct: 237 AEALGYRIKHLGVARSTASGIELRVHPTLIPADRLIANVNGVMNAVMVNGDASGSTLFYG 296

Query: 301 AGAGDGPTASAVVADLIDIARTEFGPP------YAMPATSLAAEPVAPTGERRGRAYLRF 354
           AGAG  PTAS+V+ADL+D+ R     P       A    SL+A P+ P        YLR 
Sbjct: 297 AGAGMEPTASSVIADLVDVVRAMTSDPENRVPHLAFQPDSLSAHPILPIEACESSYYLRI 356

Query: 355 TVADKVGVLAEIAAAMRDAGVSIESLIQRGAMA-DGSVLVAIVTHEVPERSIAQALEKLR 413
              D  GVLA++A+ + + G++IES++Q+     DG V + ++TH V E+SI  A+  L 
Sbjct: 357 QAKDHPGVLAQVASILSERGINIESIMQKEVEEHDGLVPMILLTHRVVEQSINDAIAALE 416

Query: 414 GSPSLAG 420
               + G
Sbjct: 417 ALQGVVG 423


Lambda     K      H
   0.319    0.136    0.388 

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: 453
Number of extensions: 15
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: 430
Length of database: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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: 51 (24.3 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