Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate GFF4491 PS417_22985 N-acetylglucosamine-6-phosphate deacetylase
Query= reanno::WCS417:GFF4491 (368 letters) >FitnessBrowser__WCS417:GFF4491 Length = 368 Score = 739 bits (1907), Expect = 0.0 Identities = 368/368 (100%), Positives = 368/368 (100%) Query: 1 MSEDNILTPDGWIRGRLVHEHGKVIAIEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIM 60 MSEDNILTPDGWIRGRLVHEHGKVIAIEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIM Sbjct: 1 MSEDNILTPDGWIRGRLVHEHGKVIAIEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIM 60 Query: 61 EGGAAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAGSARVLGVHLE 120 EGGAAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAGSARVLGVHLE Sbjct: 61 EGGAAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAGSARVLGVHLE 120 Query: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQ 180 GPYINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQ Sbjct: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQ 180 Query: 181 IGHTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVH 240 IGHTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVH Sbjct: 181 IGHTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVH 240 Query: 241 PGAMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMD 300 PGAMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMD Sbjct: 241 PGAMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMD 300 Query: 301 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG 360 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG Sbjct: 301 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG 360 Query: 361 ETIDFKNA 368 ETIDFKNA Sbjct: 361 ETIDFKNA 368 Lambda K H 0.320 0.138 0.411 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: 721 Number of extensions: 16 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 GFF4491 PS417_22985 (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.19276.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-77 244.4 0.0 1.2e-76 244.1 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4491 PS417_22985 N-acetylglucosamine- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4491 PS417_22985 N-acetylglucosamine-6-phosphate deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.1 0.0 1.2e-76 1.2e-76 53 379 .. 41 360 .. 29 361 .. 0.94 Alignments for each domain: == domain 1 score: 244.1 bits; conditional E-value: 1.2e-76 TIGR00221 53 vltpGliDvqlnGcgGvdtnd..asvetleimsealaksGvtsfLptlitredeeikkavkvareylakekn..a 123 +l+pG+iD++++G+gG+d+++ a++et+ ++ + G+ts L+t++t++ eei++ + + + ++ a lcl|FitnessBrowser__WCS417:GFF4491 41 YLLPGFIDLHVHGGGGADIMEggAAFETI---TRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAgsA 112 89******************965666776...5678899****************************9998777* PP TIGR00221 124 kiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGht 198 ++LG+hleGP++++ k Ga+p ++ + + ++ ++ +l a i+ +t+ape ++ li+ l e g+ +++Ght lcl|FitnessBrowser__WCS417:GFF4491 113 RVLGVHLEGPYINPGKLGAQP-NFAHTALMAEVEAYLRLA--PIRVITIAPEIAGHDGLIRALSERGVRMQIGHT 184 *******************86.788888766669999987..59******************************* PP TIGR00221 199 natyeelkeafkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvl 273 yee +a aG+t thlynams+l+hRepg++Ga+L+++ + +e+i D lh+hp ++r+a + + l lcl|FitnessBrowser__WCS417:GFF4491 185 LGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKF-AELIPDLLHVHPGAMRVALR--SIPCLYC 256 ******************************************775.8***************9865..5666*** PP TIGR00221 274 vtDslaaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgi 348 vtDs+aaag++++++ + ++v+ +++ ++gtlaGs+ltm ++++nlv + +++s++ + s++pa lg+ lcl|FitnessBrowser__WCS417:GFF4491 257 VTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMDQALRNLVKIG-LPISEASQRLSQFPADYLGL 330 ****************************************************99.******************** PP TIGR00221 349 ddrlGsvakGkdanLavltkdfeviltiveg 379 ++r G ++ G a+ + l++ ++ +veg lcl|FitnessBrowser__WCS417:GFF4491 331 EER-GRLQPGSFADCVRLDRSLTLTDVMVEG 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.29 // [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