GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Cupriavidus basilensis 4G11

Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate RR42_RS01160 RR42_RS01160 homoserine O-acetyltransferase

Query= SwissProt::D2Z028
         (374 letters)



>FitnessBrowser__Cup4G11:RR42_RS01160
          Length = 390

 Score =  232 bits (591), Expect = 1e-65
 Identities = 141/360 (39%), Positives = 200/360 (55%), Gaps = 13/360 (3%)

Query: 8   ASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--RPDD 65
           A + +   +   +R G +L    +  ET+G+LNAAR NAVLV   L+   H A     D 
Sbjct: 22  APQCMHFTEPLKLRNGTSLADYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYEHDP 81

Query: 66  PTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIED 125
              GWW+ MVGPGKP+DTD + VI VN+LGSC GSTGP S +P TG+PY  +FP +++ED
Sbjct: 82  RDVGWWDNMVGPGKPLDTDRFFVIGVNNLGSCFGSTGPMSANPATGQPYGATFPVVTVED 141

Query: 126 IADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAV 185
             +A A      GI++ A V+G S+GGM ALA    +P+  R  I ++        +IA 
Sbjct: 142 WVNAQARVADRFGITQFAAVMGGSLGGMQALAWSLMYPDRLRHCIVVASTPKLSAQNIAF 201

Query: 186 RSLQREAIRSDPGWLQG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERR 244
             + R AI SDP +  G +Y  G  P+RG+  AR +G +TY S ++   +FGR       
Sbjct: 202 NEVARSAILSDPDFHGGNYYAHGVKPKRGLRVARMIGHITYLSDEDMAEKFGR-----EL 256

Query: 245 RADQGRFG--PEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGA 302
           + D  RF    EF+VESYL +   +FA+ FD N+YL ++ A+D FD       GG    A
Sbjct: 257 KTDDIRFSFDVEFQVESYLRYQGDKFAEYFDANTYLLITRALDYFD--PALAFGGDLTRA 314

Query: 303 LSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362
           +S+ +    LV    TD  F  ++ +E+   L      VS+  +D P GHDAFL+D  R+
Sbjct: 315 VSQTQAS-FLVASFTTDWRFAPNRSRELVKALLDNKRPVSYAEIDAPHGHDAFLLDDPRY 373


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: 436
Number of extensions: 17
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: 390
Length adjustment: 30
Effective length of query: 344
Effective length of database: 360
Effective search space:   123840
Effective search space used:   123840
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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