GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Pseudomonas fluorescens FW300-N1B4

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Pf1N1B4_2161 Serine hydroxymethyltransferase (EC 2.1.2.1)

Query= BRENDA::R9YJZ9
         (417 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2161
          Length = 421

 Score =  590 bits (1521), Expect = e-173
 Identities = 291/420 (69%), Positives = 334/420 (79%), Gaps = 4/420 (0%)

Query: 1   MLKKAMNIADYDPELFKAIEDETRRQEEHIELIASENYTSPRVMEAQGSQLTNKYAEGYP 60
           M    + +  +D EL +AI +E  RQE+H+ELIASENY SP VM+ Q + LTNKYAEGYP
Sbjct: 1   MYDSTLTLKAFDAELCEAIHNEEHRQEDHVELIASENYASPLVMKIQSTVLTNKYAEGYP 60

Query: 61  GKRYYGGCEYVDVVETLAIERAKQLFGATYANVQPHSGSQANSAVYMALLQPGDTVLGMN 120
           GKRYY GCEYVDV E LAIER K LF   YANVQPH+G+QAN+AV++AL+ PGDTV+GMN
Sbjct: 61  GKRYYSGCEYVDVAERLAIERVKALFNCDYANVQPHAGAQANAAVFLALINPGDTVMGMN 120

Query: 121 LAHGGHLTHGSPVNFSGKLYNIIPYGID-ESGKIDYSELETLALEHKPKMIIGGFSAYSG 179
           LA GGHLTHG+P NFSG+ Y I+PYG+D E+G +DY E+E +ALE +PKM+IGGFSAYS 
Sbjct: 121 LAQGGHLTHGNPSNFSGRHYKIVPYGLDPETGFLDYDEMERIALETRPKMLIGGFSAYSR 180

Query: 180 IVDWAKLREIADKIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHKTLAGPRGGVI 239
             DWA++R IADK+GA  +VDMAHVAGLIAAG YP+P+PHAHVVTSTTHKTL GPRGG+I
Sbjct: 181 YKDWARMRAIADKVGAIFWVDMAHVAGLIAAGEYPDPLPHAHVVTSTTHKTLRGPRGGLI 240

Query: 240 LSAADDEDLYKKLNSAVFPGGQGGPLMHVIAGKAVAFKEALEPEFKTYQQQVVNNAKAMV 299
           LS   DE  YKKL+SAVFPG QGGPLMH IA KAVAFKEAL PEFKTYQ QVV NA+AM 
Sbjct: 241 LSKGQDEAFYKKLDSAVFPGVQGGPLMHQIAAKAVAFKEALRPEFKTYQTQVVINARAMA 300

Query: 300 EVFLERGYKIVSGGTDNHLMLVDLIGRELTGKEADAALGRANITVNKNSVPNDPRSPFVT 359
            V  ERGYKIVSGGTDNH+ML+DL  R  TGKEADAAL  A IT NKNSVPNDPRSPFVT
Sbjct: 301 AVLQERGYKIVSGGTDNHMMLIDLSDRPYTGKEADAALSNAYITANKNSVPNDPRSPFVT 360

Query: 360 SGVRIGTPAITRRGFKEAEARELTGWICDVLD---NAHDDAVIERVKSQVLELCARFPVY 416
           SG+RIGTPAIT RGF   E  +L GW+CDVLD   N   + V   V+ QV+ELC R PVY
Sbjct: 361 SGLRIGTPAITTRGFGVIECEQLAGWLCDVLDALENGDSERVGHHVREQVVELCRRHPVY 420


Lambda     K      H
   0.316    0.135    0.393 

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: 633
Number of extensions: 28
Number of successful extensions: 3
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: 417
Length of database: 421
Length adjustment: 32
Effective length of query: 385
Effective length of database: 389
Effective search space:   149765
Effective search space used:   149765
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: 41 (21.6 bits)
S2: 50 (23.9 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