Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate AO353_04450 AO353_04450 N-acetylglucosamine-6-phosphate deacetylase
Query= reanno::pseudo3_N2E3:AO353_04450 (368 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04450 Length = 368 Score = 744 bits (1922), Expect = 0.0 Identities = 368/368 (100%), Positives = 368/368 (100%) Query: 1 MSEDNILTAQGWIRGRLIHEHGKIVRIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM 60 MSEDNILTAQGWIRGRLIHEHGKIVRIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM Sbjct: 1 MSEDNILTAQGWIRGRLIHEHGKIVRIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM 60 Query: 61 EGTPAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEFCEQRPKGCARVLGVHLE 120 EGTPAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEFCEQRPKGCARVLGVHLE Sbjct: 61 EGTPAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEFCEQRPKGCARVLGVHLE 120 Query: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDKLIRALSDRGIRMQ 180 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDKLIRALSDRGIRMQ Sbjct: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDKLIRALSDRGIRMQ 180 Query: 181 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH 240 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH Sbjct: 181 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH 240 Query: 241 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD 300 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD Sbjct: 241 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD 300 Query: 301 QALRNLVKIGLPLAEASQRLSQFPADYLGIQERGRLQPGAWADCVRLDRSLTLTAVMVEG 360 QALRNLVKIGLPLAEASQRLSQFPADYLGIQERGRLQPGAWADCVRLDRSLTLTAVMVEG Sbjct: 301 QALRNLVKIGLPLAEASQRLSQFPADYLGIQERGRLQPGAWADCVRLDRSLTLTAVMVEG 360 Query: 361 EDIDFKNA 368 EDIDFKNA Sbjct: 361 EDIDFKNA 368 Lambda K H 0.320 0.138 0.416 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: 716 Number of extensions: 19 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 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: 49 (23.5 bits)
Align candidate AO353_04450 AO353_04450 (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.30335.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-79 254.1 0.0 1.3e-79 253.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 AO353_04450 N-acetylglucosamine- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 AO353_04450 N-acetylglucosamine-6-phosphate deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.8 0.0 1.3e-79 1.3e-79 52 379 .. 40 360 .. 15 361 .. 0.94 Alignments for each domain: == domain 1 score: 253.8 bits; conditional E-value: 1.3e-79 TIGR00221 52 nvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredeeikkavkvarey 116 +l+pG+iD++++G+gG d+++ + +++ + ++ + G+ts L+t++t++ eei++ + + e+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 40 PYLLPGFIDLHVHGGGGKDIMEGT-PAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEF 103 589******************854.67788889999***************************** PP TIGR00221 117 lakekn..akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekqt 179 + + a++LG+hleGP++++ k Ga+p ++ + + ++ ++ +l a i+ +t+ape ++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 104 CEQRPKgcARVLGVHLEGPYINPGKLGAQP-NFAHTALMAEVEAYLALA--PIRVITIAPEIAGH 165 *9998879********************86.788887666658888766..6************* PP TIGR00221 180 aelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvv 244 +li+ l + gi +++Ght yee +a +aG++ thlynams+l+hRepg++Ga+L++ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 166 DKLIRALSDRGIRMQIGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAH-AKY 229 *************************************************************.679 PP TIGR00221 245 teiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtl 309 +e+i D lh+hp +ir+a + + l vtDs+aaag++++++ + ++v+ +++ +gtl lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 230 AELIPDLLHVHPGAIRVALR--SIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTL 292 ****************9966..5566*************************************** PP TIGR00221 310 aGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374 aGs+ltm ++++nlv + ++l+++ + s++pa lgi++r G ++ G a+ + l++ ++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 293 AGSTLTMDQALRNLVKIG-LPLAEASQRLSQFPADYLGIQER-GRLQPGAWADCVRLDRSLTLTA 355 ****************99.***********************.********************** PP TIGR00221 375 tiveg 379 +veg lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 356 VMVEG 360 ***98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (368 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.59 // [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