GapMind for Amino acid biosynthesis

 

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

Align serine O-acetyltransferase (EC 2.3.1.30); homoserine O-acetyltransferase (EC 2.3.1.31) (characterized)
to candidate AO356_13410 AO356_13410 homoserine O-acetyltransferase

Query= BRENDA::D2Z028
         (374 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13410
          Length = 379

 Score =  233 bits (594), Expect = 7e-66
 Identities = 133/347 (38%), Positives = 194/347 (55%), Gaps = 8/347 (2%)

Query: 19  AMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRP--DDPTPGWWEAMVG 76
           A+  G +L    + YET+G+LNA   NAVL+   LS   HAA     DD  PGWW++ +G
Sbjct: 25  ALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSIDDRKPGWWDSCIG 84

Query: 77  PGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRA 136
           PGKP+DT  + V+ +N+LG C GSTGP+S +P TG+P+   FP L++ED   + A     
Sbjct: 85  PGKPIDTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPVLTVEDWVHSQARLADR 144

Query: 137 LGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSD 196
           LGI + A V+G S+GGM AL     +P+  R  ++++ A      +IA   + R+AI +D
Sbjct: 145 LGIGQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSAQNIAFNEVARQAILTD 204

Query: 197 PGWLQGHYDE-GEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEF 255
           P +  G + E G  P+RG++ AR +G +TY S      +FGR    E+   D      EF
Sbjct: 205 PEFHGGSFQEHGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKSEKLNYD--FHSVEF 262

Query: 256 EVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMG 315
           +VESYL +  + F+ RFD N+YL ++ A+D FD             A +     +  VM 
Sbjct: 263 QVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDNLAKTFANA---TAKFCVMS 319

Query: 316 ARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362
             TD  F  ++ +E+ D L A   DV +L +D P GHDAFL+ I R+
Sbjct: 320 FTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRY 366


Lambda     K      H
   0.321    0.138    0.427 

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: 440
Number of extensions: 20
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: 374
Length of database: 379
Length adjustment: 30
Effective length of query: 344
Effective length of database: 349
Effective search space:   120056
Effective search space used:   120056
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.

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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