GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Phaeobacter inhibens BS107

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.-; EC 1.2.1.103 (characterized, see rationale)
to candidate GFF1682 PGA1_c17050 N-acetyl-gamma-glutamyl-phosphate reductase ArgC

Query= uniprot:Q5JFW1
         (330 letters)



>FitnessBrowser__Phaeo:GFF1682
          Length = 342

 Score =  222 bits (566), Expect = 9e-63
 Identities = 146/346 (42%), Positives = 192/346 (55%), Gaps = 26/346 (7%)

Query: 3   KAAVVGASGYIGGELVRLLAMHPEVEITAITSRRFAGQKVHKVHPNLRGLDLR-FTNTKE 61
           K A++GASGY G ELVRL++ HP +EI A+++ R AG  + +V P+LR L+L       E
Sbjct: 4   KVAILGASGYTGAELVRLISQHPTIEIAALSAERKAGMTMAQVFPHLRHLELPVLCKIGE 63

Query: 62  FD---ADVIFLAVPHGTSMEIIDDYLGSAKIIDMSADFRLRE-DLYREYYGE-HKRPELI 116
            D    D+ F A+PH TS E+I       KI+D+SADFRLR+ D Y ++YG  H      
Sbjct: 64  IDFTGIDLCFCALPHKTSQEVIAALPQDLKIVDLSADFRLRDPDEYEKWYGNPHAALAQQ 123

Query: 117 EEFVYGLPELHRKEIRKAELVANPGCNATATILALYPFREL----TDEAIVDLKVSSSAG 172
           +E VYGL E +R+EI+ A LVA  GCNA     AL P         D+ I+DLK + S  
Sbjct: 124 KEAVYGLSEFYREEIKSARLVAGTGCNAATGQFALRPLIASGVIDLDDIILDLKCAVSGA 183

Query: 173 GRRENVASIHPERSHVVRVYKPYH-HRHEGEVIQETG------VKAAFTVHSVDIIRGLL 225
           GR      +H E S     Y     HRH GE  QE        VK  FT H V   RG+L
Sbjct: 184 GRSLKENLLHAELSEGYHGYAVGGTHRHLGEFDQEFSKIAGRPVKVQFTPHLVPANRGIL 243

Query: 226 ATIYFRFEGSTRELLRKLLV--YKDEPFVRLVTDKGGLQRFPDPKYVIGSNFADIGFAHD 283
           AT+Y + +  T   + + L   Y DEPF+ L+         P  +++ GSNF  IG A D
Sbjct: 244 ATVYVKGDAQT---IHQTLATAYADEPFIELLP----FGEAPSTRHIRGSNFCHIGVAAD 296

Query: 284 EENSRAIVLSAIDNLIKGGSGQAVQNMNLMFGLDERTGLNYYPVYP 329
               R IV++A+DNL KG SGQA+QN NLM G +E TGL   P++P
Sbjct: 297 RIEGRTIVIAALDNLTKGSSGQALQNANLMLGEEETTGLMMAPLFP 342


Lambda     K      H
   0.321    0.140    0.404 

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: 311
Number of extensions: 22
Number of successful extensions: 6
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: 330
Length of database: 342
Length adjustment: 28
Effective length of query: 302
Effective length of database: 314
Effective search space:    94828
Effective search space used:    94828
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: 49 (23.5 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