Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate Ga0059261_1645 Ga0059261_1645 N-acetylglucosamine-6-phosphate deacetylase
Query= reanno::Korea:Ga0059261_1645 (386 letters) >FitnessBrowser__Korea:Ga0059261_1645 Length = 386 Score = 771 bits (1991), Expect = 0.0 Identities = 386/386 (100%), Positives = 386/386 (100%) Query: 1 MRIRLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGVERKIDLGGGWLLPGFIDTQV 60 MRIRLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGVERKIDLGGGWLLPGFIDTQV Sbjct: 1 MRIRLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGVERKIDLGGGWLLPGFIDTQV 60 Query: 61 NGGGGVLFNDQADVDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP 120 NGGGGVLFNDQADVDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP Sbjct: 61 NGGGGVLFNDQADVDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP 120 Query: 121 GVVGIHVEGPFINEVKRGIHEARRIRRLDADTLALFTAPRRGRVMLTLAPELCDTDDVRT 180 GVVGIHVEGPFINEVKRGIHEARRIRRLDADTLALFTAPRRGRVMLTLAPELCDTDDVRT Sbjct: 121 GVVGIHVEGPFINEVKRGIHEARRIRRLDADTLALFTAPRRGRVMLTLAPELCDTDDVRT 180 Query: 181 LVKHGVIVSAGHTNATYDEMMAAIGAGLTGFTHLFNAMSPLHHRNPGAVGAAFDSESWCG 240 LVKHGVIVSAGHTNATYDEMMAAIGAGLTGFTHLFNAMSPLHHRNPGAVGAAFDSESWCG Sbjct: 181 LVKHGVIVSAGHTNATYDEMMAAIGAGLTGFTHLFNAMSPLHHRNPGAVGAAFDSESWCG 240 Query: 241 MIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPSVGTGDTEFMLQGKRIMVRNGVCLFED 300 MIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPSVGTGDTEFMLQGKRIMVRNGVCLFED Sbjct: 241 MIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPSVGTGDTEFMLQGKRIMVRNGVCLFED 300 Query: 301 GTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLDRYGALAPGKRADWVWLD 360 GTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLDRYGALAPGKRADWVWLD Sbjct: 301 GTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLDRYGALAPGKRADWVWLD 360 Query: 361 KDLQPRGTWIGGEPVADAEEFARAAQ 386 KDLQPRGTWIGGEPVADAEEFARAAQ Sbjct: 361 KDLQPRGTWIGGEPVADAEEFARAAQ 386 Lambda K H 0.321 0.137 0.413 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: 694 Number of extensions: 10 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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)
Align candidate Ga0059261_1645 Ga0059261_1645 (N-acetylglucosamine-6-phosphate deacetylase)
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))
# 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.carbon/TIGR00221.hmm # target sequence database: /tmp/gapView.3844.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00221 [M=380] Accession: TIGR00221 Description: nagA: N-acetylglucosamine-6-phosphate deacetylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-95 306.2 0.0 1.7e-95 306.1 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1645 Ga0059261_1645 N-acetylglucosami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_1645 Ga0059261_1645 N-acetylglucosamine-6-phosphate deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 306.1 0.0 1.7e-95 1.7e-95 6 379 .. 4 372 .. 1 373 [. 0.95 Alignments for each domain: == domain 1 score: 306.1 bits; conditional E-value: 1.7e-95 TIGR00221 6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 l++ +i+t + vld + v ++d+ i a+++ + ++idl g l+pG+iD q+nG+gGv +nd+ lcl|FitnessBrowser__Korea:Ga0059261_1645 4 RLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGV-ERKIDLGGGWLLPGFIDTQVNGGGGVLFNDQ 71 6899************************999877655.578***************************8 PP TIGR00221 75 sv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGa 142 + +++ + a a+ G+t+fLptli+ ++i a+ ++ +++ + ++G+h+eGPf++ +k+G+ lcl|FitnessBrowser__Korea:Ga0059261_1645 72 ADvDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP-GVVGIHVEGPFINEVKRGI 139 877****************************************999877.8****************** PP TIGR00221 143 hpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafka 211 h+ ir+ d++ l f + + ++tlape+ ++ +++l+++g+ivsaGhtnaty+e+ +a+ a lcl|FitnessBrowser__Korea:Ga0059261_1645 140 HEARRIRRLDADTLALFTAPRRGRV-MLTLAPELC-DTDDVRTLVKHGVIVSAGHTNATYDEMMAAIGA 206 *************999998888876.69****665.5666799************************** PP TIGR00221 212 GitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaa 280 G t thl+nams+l+hR+pg++Ga+ d+ + +++i+D h hp+ +rla ++kg+ +l+lvtD++ + lcl|FitnessBrowser__Korea:Ga0059261_1645 207 GLTGFTHLFNAMSPLHHRNPGAVGAAFDS-ESWCGMIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPS 274 ****************************9.889************************************ PP TIGR00221 281 agaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgid 349 g+ + +f+ +Gk +++r++ +l ++gtlaG+ l m +++n ve +++s+ dv+ ++s pa+ l +d lcl|FitnessBrowser__Korea:Ga0059261_1645 275 VGTGDTEFMLQGKRIMVRNGVCLFEDGTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLD 343 *******************************************************************97 PP TIGR00221 350 drlGsvakGkdanLavltkdfeviltiveg 379 r G++a Gk a+ + l+kd + +t + g lcl|FitnessBrowser__Korea:Ga0059261_1645 344 -RYGALAPGKRADWVWLDKDLQPRGTWIGG 372 .55******************998887765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (386 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: 00:00:00.01 # Mc/sec: 11.54 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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