Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_011385407.1 AMB_RS15270 serine O-acetyltransferase
Query= BRENDA::P95231 (229 letters) >NCBI__GCF_000009985.1:WP_011385407.1 Length = 263 Score = 216 bits (550), Expect = 3e-61 Identities = 107/202 (52%), Positives = 148/202 (73%), Gaps = 5/202 (2%) Query: 4 AMRGDIRAARERDPAAPTALEVIFCYPGVHAVWGHRLAHWLWQRGARLLARAAAEFTRIL 63 +++ DI + R+RDPAA + LEV+ CYPG+HA+ HRL++W W RG R+L R + +IL Sbjct: 5 SLQEDIASIRKRDPAAHSWLEVLLCYPGLHALMFHRLSNWCWNRGLRVLGRFVSHVGKIL 64 Query: 64 TGVDIHPGAVIGARVFIDHATGVVIGETAEVGDDVTIYHGVTLGGSGMVGGKRHPTVGDR 123 TG++IHP A +G R FIDH TGVVIGETA +G DVTIYHGVTLGG+ + GKRHPT+ D Sbjct: 65 TGIEIHPAAQLGPRFFIDHGTGVVIGETAVIGADVTIYHGVTLGGTSLHKGKRHPTLEDG 124 Query: 124 VIIGAGAKVLGPIKIGEDSRIGANAVVVKPVPPSAVVVGVPGQVIGQSQPSP----GGPF 179 VI+G+GA+VLGPI +G+ +RIGANAVV+ VPP +VG+P +++ + Q + G P Sbjct: 125 VIVGSGAQVLGPITVGKGARIGANAVVLTDVPPGVTMVGIPARMVMRRQDADFCAYGLPV 184 Query: 180 DWRLPDLVGASLDSLLTRVARL 201 + LPD V ++DS+ ++VA L Sbjct: 185 E-DLPDPVVRAIDSVRSQVATL 205 Lambda K H 0.321 0.141 0.443 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: 224 Number of extensions: 16 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: 229 Length of database: 263 Length adjustment: 24 Effective length of query: 205 Effective length of database: 239 Effective search space: 48995 Effective search space used: 48995 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: 46 (22.3 bits)
Align candidate WP_011385407.1 AMB_RS15270 (serine O-acetyltransferase)
to HMM TIGR01172 (cysE: serine O-acetyltransferase (EC 2.3.1.30))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01172.hmm # target sequence database: /tmp/gapView.23535.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01172 [M=162] Accession: TIGR01172 Description: cysE: serine O-acetyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-78 247.0 1.8 4.8e-78 246.9 1.0 1.4 2 lcl|NCBI__GCF_000009985.1:WP_011385407.1 AMB_RS15270 serine O-acetyltrans Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385407.1 AMB_RS15270 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.9 1.0 4.8e-78 4.8e-78 2 162 .] 7 167 .. 6 167 .. 0.99 2 ? -3.8 0.0 0.59 0.59 47 68 .. 201 222 .. 198 226 .. 0.77 Alignments for each domain: == domain 1 score: 246.9 bits; conditional E-value: 4.8e-78 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaaki 70 +ed+ ++++rDPaa+s+levll+y+glhal+ +rl+++ ++r+l++l+r++s++ ++ltg++ihPaa++ lcl|NCBI__GCF_000009985.1:WP_011385407.1 7 QEDIASIRKRDPAAHSWLEVLLCYPGLHALMFHRLSNWCWNRGLRVLGRFVSHVGKILTGIEIHPAAQL 75 79******************************************************************* PP TIGR01172 71 grgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenak 139 g +++iDh+tGvviGetavig dv+iy+gvtLGgt+ +kgkRhPt+++gv++g+ga+vLG+i+vg++a+ lcl|NCBI__GCF_000009985.1:WP_011385407.1 76 GPRFFIDHGTGVVIGETAVIGADVTIYHGVTLGGTSLHKGKRHPTLEDGVIVGSGAQVLGPITVGKGAR 144 ********************************************************************* PP TIGR01172 140 iGansvvlkdvpaeatvvGvpar 162 iGan+vvl+dvp+++t+vG+par lcl|NCBI__GCF_000009985.1:WP_011385407.1 145 IGANAVVLTDVPPGVTMVGIPAR 167 *********************97 PP == domain 2 score: -3.8 bits; conditional E-value: 0.59 TIGR01172 47 llarllselvrvltgvdihPaa 68 +a+l++++ ++ t++ hP+ lcl|NCBI__GCF_000009985.1:WP_011385407.1 201 QVATLMERIKELETELHGHPTQ 222 5788888888999999989875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (263 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.95 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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