GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Marinobacter adhaerens HP15

Align serine O-acetyltransferase (EC 2.3.1.30); homoserine O-acetyltransferase (EC 2.3.1.31) (characterized)
to candidate GFF285 HP15_284 homoserine O-acetyltransferase

Query= BRENDA::D2Z028
         (374 letters)



>FitnessBrowser__Marino:GFF285
          Length = 382

 Score =  219 bits (557), Expect = 1e-61
 Identities = 130/343 (37%), Positives = 190/343 (55%), Gaps = 9/343 (2%)

Query: 23  GGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--RPDDPTPGWWEAMVGPGKP 80
           G +L    +  ET+G+LNA   NAVL+   LS   HAA     +D  PGWW++ +GPGKP
Sbjct: 29  GQSLENYDLVVETYGTLNADASNAVLICHALSGHHHAAGYHSAEDRKPGWWDSCIGPGKP 88

Query: 81  VDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGIS 140
           +DTD + V+ +N+LG C GSTGP S +P TG+P+   FP +++ D   + A     LGI 
Sbjct: 89  IDTDRFFVVSLNNLGGCHGSTGPNSINPETGKPFGPEFPVITVGDWVKSQALLADRLGIQ 148

Query: 141 RLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWL 200
             A VVG S+GGM AL     +P+  R  + ++        +IA   + R+AI SD  + 
Sbjct: 149 CWAAVVGGSLGGMQALQWSLDYPDRLRHAVVIASTPRLTAQNIAFNEVARQAITSDREFH 208

Query: 201 QG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVES 259
            G +YD    PRRG++ AR +G +TY S      +FGR     R +A +  +  EF+VES
Sbjct: 209 DGRYYDFDTVPRRGLMLARMVGHITYLSDASMGEKFGREL---RDQAYKFGYDAEFQVES 265

Query: 260 YLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTD 319
           YL +  +RF++ FD N+YL ++ A+D FD       GG    AL+    E  LV+   TD
Sbjct: 266 YLRYQGERFSESFDANTYLLMTRALDYFD--PAYEFGGDLSKALAAASCE-YLVLSFSTD 322

Query: 320 ILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362
             F  ++ +E+ + +      VS+  VD P GHDAFL+   R+
Sbjct: 323 WRFTPARSEEMVNAMIGARRKVSYAEVDAPWGHDAFLIPTPRY 365


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: 455
Number of extensions: 29
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: 382
Length adjustment: 30
Effective length of query: 344
Effective length of database: 352
Effective search space:   121088
Effective search space used:   121088
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