Align amino-acid acetyltransferase (characterized)
to candidate WP_004149616.1 KVAR_RS04235 amino-acid N-acetyltransferase
Query= CharProtDB::CH_024150 (443 letters) >NCBI__GCF_000025465.1:WP_004149616.1 Length = 443 Score = 818 bits (2114), Expect = 0.0 Identities = 417/442 (94%), Positives = 427/442 (96%) Query: 1 MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLV 60 MVKER+TELVEGFRHSVPYIN HRGKTFVIMLGGEAIEHENFS+IVNDIGLLHSLGIRLV Sbjct: 1 MVKERRTELVEGFRHSVPYINAHRGKTFVIMLGGEAIEHENFSNIVNDIGLLHSLGIRLV 60 Query: 61 VVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTP 120 VVYGARPQIDANLA HHHEP+YHK RVTDAKTLELVKQAAG LQL+ITARLSMSLNNTP Sbjct: 61 VVYGARPQIDANLAEHHHEPVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTP 120 Query: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSV 180 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDE+AIHRQLDSGAIVLMGPVAVSV Sbjct: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEEAIHRQLDSGAIVLMGPVAVSV 180 Query: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEK 240 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGV N G+IVSELFPNEAQARVE E Sbjct: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQAGEIVSELFPNEAQARVEELEAD 240 Query: 241 GDYNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR 300 DYNSGTVRFLRGAVKACRSGVRRCHLISYQE+GALLQELFSRDGIGTQIVMESAEQIRR Sbjct: 241 EDYNSGTVRFLRGAVKACRSGVRRCHLISYQENGALLQELFSRDGIGTQIVMESAEQIRR 300 Query: 301 ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI 360 ATINDIGGILELI PLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI Sbjct: 301 ATINDIGGILELISPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI 360 Query: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDL 420 GEMACVAVHPDYRSSSRGEVLLERIAAQA+Q GLSKLFVLTTRSIHWFQERGFTPVDIDL Sbjct: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQARQMGLSKLFVLTTRSIHWFQERGFTPVDIDL 420 Query: 421 LPESKKQLYNYQRKSKVLMADL 442 LPESKKQ+YNYQR+SKVLMADL Sbjct: 421 LPESKKQMYNYQRRSKVLMADL 442 Lambda K H 0.319 0.136 0.384 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: 775 Number of extensions: 12 Number of successful extensions: 1 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: 443 Length of database: 443 Length adjustment: 32 Effective length of query: 411 Effective length of database: 411 Effective search space: 168921 Effective search space used: 168921 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: 51 (24.3 bits)
Align candidate WP_004149616.1 KVAR_RS04235 (amino-acid N-acetyltransferase)
to HMM TIGR01890 (argA: amino-acid N-acetyltransferase (EC 2.3.1.1))
# 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/TIGR01890.hmm # target sequence database: /tmp/gapView.1171127.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01890 [M=429] Accession: TIGR01890 Description: N-Ac-Glu-synth: amino-acid N-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-202 657.0 1.2 7.6e-202 656.8 1.2 1.0 1 NCBI__GCF_000025465.1:WP_004149616.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025465.1:WP_004149616.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 656.8 1.2 7.6e-202 7.6e-202 1 429 [] 9 442 .. 9 442 .. 0.99 Alignments for each domain: == domain 1 score: 656.8 bits; conditional E-value: 7.6e-202 TIGR01890 1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtth 73 +v+++r++ Pyinahr+kt+v++lgge++e++n++++v+di+llhslG+rlv+v+Garpqi+ +la+++ ++ NCBI__GCF_000025465.1:WP_004149616.1 9 LVEGFRHSVPYINAHRGKTFVIMLGGEAIEHENFSNIVNDIGLLHSLGIRLVVVYGARPQIDANLAEHHHEPV 81 699********************************************************************** PP TIGR01890 74 yvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevr 146 y++ rvtd+ +lelvk+aaG l+l+i+arlsmsl+ntp +g++++vvsGnf++a+P+Gv++Gvdy+h+G++r NCBI__GCF_000025465.1:WP_004149616.1 82 YHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTPLQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIR 154 ************************************************************************* PP TIGR01890 147 kidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsa 219 +id e+i+r+ld++ ivl++P++ svtGe fnl++e++at+ aiklka+k+i +++++G+ ++ G++v el++ NCBI__GCF_000025465.1:WP_004149616.1 155 RIDEEAIHRQLDSGAIVLMGPVAVSVTGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQAGEIVSELFP 227 ************************************************************************* PP TIGR01890 220 qeveslverleeet.....tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesire 287 +e+++ ve+le + t r+l+ avka+r+Gv+r+hl+sy+e+Gallqelf+rdGiGt++++e++e+ir+ NCBI__GCF_000025465.1:WP_004149616.1 228 NEAQARVEELEADEdynsgTVRFLRGAVKACRSGVRRCHLISYQENGALLQELFSRDGIGTQIVMESAEQIRR 300 **********9998899*9****************************************************** PP TIGR01890 288 atiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPear 360 ati+d+ggileli+Ple+qGilvrrsre+le ei++f++i++d + i+caalyp++ee++ge+ac+av+P++r NCBI__GCF_000025465.1:WP_004149616.1 301 ATINDIGGILELISPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMACVAVHPDYR 373 ************************************************************************* PP TIGR01890 361 dggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429 + rGe ll++i ++arq+Gl++lfvlttr+ hWf+erGf+++++d lPe+++++ynyqrrsk+l+ l NCBI__GCF_000025465.1:WP_004149616.1 374 SSSRGEVLLERIAAQARQMGLSKLFVLTTRSIHWFQERGFTPVDIDLLPESKKQMYNYQRRSKVLMADL 442 *****************************************************************9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (429 nodes) Target sequences: 1 (443 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.36 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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