Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate H281DRAFT_05506 H281DRAFT_05506 N-acetylglucosamine 6-phosphate deacetylase (EC 3.5.1.25)
Query= reanno::WCS417:GFF4491 (368 letters) >FitnessBrowser__Burk376:H281DRAFT_05506 Length = 376 Score = 410 bits (1055), Expect = e-119 Identities = 202/363 (55%), Positives = 268/363 (73%), Gaps = 4/363 (1%) Query: 5 NILTPDGWIRGRLVHEHGKVIA-IEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIMEGG 63 NILTP GW+ GR+V + +IA IEG+P Y+LPGFIDLHVHGGGG D+M+G Sbjct: 3 NILTPKGWVLGRVVVDAAGLIARIEGSPVTSPLLAAGYVLPGFIDLHVHGGGGTDLMDGE 62 Query: 64 AAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCER-RPAGSARVLGVHLEGP 122 A + +TH +GTTS LATTMTAP +++ G LG + R G +R+LGVHLEGP Sbjct: 63 TAACVVAKTHAEYGTTSFLATTMTAPEDDLRVATGHLGAAIRKPRGPGQSRILGVHLEGP 122 Query: 123 YINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQIG 182 ++N K G+QP A AE++ L +A +R++T+APEI G +IR L ERG+R+Q+G Sbjct: 123 FLNANKRGSQPAHTRCAAPAELDELLNIAHVRLVTLAPEIEGQLAIIRKLVERGIRVQLG 182 Query: 183 HTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVHPG 242 H+ G+YE+G+AAL GAT F HL+NAMS +HHR+PGIVG A AHA++AE+IPDLLHVHPG Sbjct: 183 HSTGTYEQGLAALQCGATGFAHLFNAMSGMHHRDPGIVGVAFAHAEYAEMIPDLLHVHPG 242 Query: 243 AMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTV--TKCLGGVRLADGTLAGSTLTMD 300 A++ A R+IP LYC+TDS +A GM +GE+ LG+ V +C GVRLADGTLA STLTMD Sbjct: 243 AVKAAFRAIPKLYCITDSCSAVGMGEGEFTLGAQKVFRRRCESGVRLADGTLAASTLTMD 302 Query: 301 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG 360 +ALRNLV +G+ I++AS RLS+FPAD+LGL++RGRL PG++ D V L ++L L +V +EG Sbjct: 303 EALRNLVSLGMTIADASDRLSRFPADFLGLQDRGRLVPGAWGDYVALSQNLALEEVCIEG 362 Query: 361 ETI 363 E + Sbjct: 363 EHV 365 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: 510 Number of extensions: 24 Number of successful extensions: 4 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: 376 Length adjustment: 30 Effective length of query: 338 Effective length of database: 346 Effective search space: 116948 Effective search space used: 116948 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 H281DRAFT_05506 H281DRAFT_05506 (N-acetylglucosamine 6-phosphate deacetylase (EC 3.5.1.25))
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.26375.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-74 235.7 0.0 5.1e-74 235.4 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_05506 H281DRAFT_05506 N-acetylglucosam Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_05506 H281DRAFT_05506 N-acetylglucosamine 6-phosphate deacetylase (EC 3.5.1.25 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.4 0.0 5.1e-74 5.1e-74 50 379 .. 37 362 .. 25 363 .. 0.93 Alignments for each domain: == domain 1 score: 235.4 bits; conditional E-value: 5.1e-74 TIGR00221 50 kgnvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredeeikkavkvare 115 + +++pG+iD++++G+gG+d +d + + ++ ++ a++G+tsfL+t++t+++++++ a + lcl|FitnessBrowser__Burk376:H281DRAFT_05506 37 AAGYVLPGFIDLHVHGGGGTDLMDGETAAC-VVAKTHAEYGTTSFLATTMTAPEDDLRVATGHLGA 101 56799*******************776554.6789999**************************** PP TIGR00221 116 ylakekn...akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekq 178 ++ k ++ ++iLG+hleGPfl+ +k+G +p + + +el ++l+ +++ vtlape ++ lcl|FitnessBrowser__Burk376:H281DRAFT_05506 102 AIRKPRGpgqSRILGVHLEGPFLNANKRGSQPAHTRCAAPAEL-DELLNI--AHVRLVTLAPEIEG 164 ***99988889*******************9987766667777.888865..59************ PP TIGR00221 179 taelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvv 244 + +i+kl+e gi v++Gh+ tye+ +a + G+t hl+nams ++hR+pg++G + ++++ + lcl|FitnessBrowser__Burk376:H281DRAFT_05506 165 QLAIIRKLVERGIRVQLGHSTGTYEQGLAALQCGATGFAHLFNAMSGMHHRDPGIVGVAFAHAE-Y 229 **************************************************************65.9 PP TIGR00221 245 teiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyir..edtlldkngt 308 +e+i D lh+hp +++ a+++ + kl +tDs +a g+ ++f+ + ++v+ r e ++ ++gt lcl|FitnessBrowser__Burk376:H281DRAFT_05506 230 AEMIPDLLHVHPGAVKAAFRA--IPKLYCITDSCSAVGMGEGEFTLGAQKVFRRrcESGVRLADGT 293 9*****************987..678*************************98844566777**** PP TIGR00221 309 laGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374 la s+ltm e+++nlv + ++++d+ s +pa lg++dr G + G + ++l+++ + lcl|FitnessBrowser__Burk376:H281DRAFT_05506 294 LAASTLTMDEALRNLVSLG-MTIADASDRLSRFPADFLGLQDR-GRLVPGAWGDYVALSQNLALEE 357 *****************99.***********************.******************9999 PP TIGR00221 375 tiveg 379 +eg lcl|FitnessBrowser__Burk376:H281DRAFT_05506 358 VCIEG 362 98887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (376 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: 8.90 // [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