Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate SMc02878 SMc02878 N-acetylglucosamine-6-phosphate deacetylase
Query= reanno::MR1:202606 (378 letters) >FitnessBrowser__Smeli:SMc02878 Length = 386 Score = 314 bits (804), Expect = 3e-90 Identities = 182/382 (47%), Positives = 234/382 (61%), Gaps = 9/382 (2%) Query: 2 KFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTA----LGAKEVRYTGTL-VPGFIDVQV 56 K T+ ++FDG +H + IE G + + A G + + G L VPGFID+QV Sbjct: 4 KKTISGARIFDGIDWHDGAALVIEAGHVKAIAPAGSVPAGGETIDARGLLLVPGFIDLQV 63 Query: 57 NGGGGALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSA 116 NGGGGAL N P++ I I AHA+FGTT LPTLITD V A A A A Sbjct: 64 NGGGGALLNEKPSLESIRQICAAHAQFGTTALLPTLITDTRAVRTAAIAAGIEAKAAAVP 123 Query: 117 GVLGVHFEGPHLSVPKKGVHPQGFIREITEAELA--IFCRQDLGIRVVTLAPENVSPEVI 174 G LG+H EGPHLSV +KG H IR + + +LA + C + L ++T+APEN + E + Sbjct: 124 GFLGLHLEGPHLSVARKGAHDPALIRPMGDDDLAEILACAKALSRLMLTVAPENATKEQV 183 Query: 175 RLLVESGVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETA 234 R L ++GV V LGH++ DYDT A KAGA THL+NAMS LG REPGVVGAA+ + T Sbjct: 184 RALADAGVVVSLGHTDVDYDTACAYAKAGARTVTHLFNAMSGLGHREPGVVGAALSTGTL 243 Query: 235 WCGLIVDGHHVHPAAARIALRAKP-RGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDR 293 G+I DG HVHPA+ IALR K G++ LVTDAM P+G D+TSF L G ++LR G R Sbjct: 244 HAGMIADGFHVHPASMGIALRGKKGPGQIFLVTDAMSPIG-TDQTSFFLNGREILRQGGR 302 Query: 294 LNAVTGELAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRA 353 L G LAG +DM S+V LGLP+ EA+RMA+ YPA+ +GIA GRL G A Sbjct: 303 LTLADGTLAGADVDMLSSVRFVHQKLGLPIEEAVRMASAYPADAMGIASHKGRLLPGTDA 362 Query: 354 DLVLLDNQYQVLANYIAGNAVY 375 D VLL + + + +I G V+ Sbjct: 363 DFVLLTPELAMKSTWIGGETVF 384 Lambda K H 0.321 0.137 0.400 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: 423 Number of extensions: 15 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: 378 Length of database: 386 Length adjustment: 30 Effective length of query: 348 Effective length of database: 356 Effective search space: 123888 Effective search space used: 123888 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 SMc02878 SMc02878 (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.18912.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-93 299.2 0.0 2.3e-93 299.1 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc02878 SMc02878 N-acetylglucosamine-6-p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02878 SMc02878 N-acetylglucosamine-6-phosphate deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 299.1 0.0 2.3e-93 2.3e-93 3 379 .. 3 380 .. 1 381 [. 0.95 Alignments for each domain: == domain 1 score: 299.1 bits; conditional E-value: 2.3e-93 TIGR00221 3 eslllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv. 76 + + +i+ + d d a vi+ + +ka+ + + + ++id++g l pG+iD+q+nG+gG+ n++ + lcl|FitnessBrowser__Smeli:SMc02878 3 AKKTISGARIFDGIDWHDGAALVIEAGHVKAIAPAGSVPAGGETIDARGLLLVPGFIDLQVNGGGGALLNEKPSl 77 5566788899************************************************************96555 PP TIGR00221 77 etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirep 151 e++ + a a+ G+t+ Lptlit + a+ + +e++a+ LGlhleGP+ls+ +kGah + ir+ lcl|FitnessBrowser__Smeli:SMc02878 78 ESIRQICAAHAQFGTTALLPTLITDTRAVRTAAIAAGIEAKAAAVP-GFLGLHLEGPHLSVARKGAHDPALIRPM 151 *****************************************99988.8*************************98 PP TIGR00221 152 .dvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamsk 225 d +l + + ++ + ++t+ap e+ t e ++ l++ag++vs+Ght+ +y+++ + +kaG+ +thl+nams lcl|FitnessBrowser__Smeli:SMc02878 152 gDDDLAEILACAKALSRLMLTVAP-ENATKEQVRALADAGVVVSLGHTDVDYDTACAYAKAGARTVTHLFNAMSG 225 35667666777777777889****.999*********************************************** PP TIGR00221 226 ldhRepgviGavLdeddvvteiiaDGlhihpknirlakk.lkgdsklvlvtDslaaagaklekfifaGkevyire 299 l hRepgv+Ga+L + + +++iaDG h+hp+ + +a + kg ++ lvtD++++ g++ +f +G+e+ ++ lcl|FitnessBrowser__Smeli:SMc02878 226 LGHREPGVVGAALSTGTLHAGMIADGFHVHPASMGIALRgKKGPGQIFLVTDAMSPIGTDQTSFFLNGREILRQG 300 **********************************99866267999****************************** PP TIGR00221 300 dtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374 ++l ++gtlaG+ + m+ +v+ + +++++++vr++s +pa a+gi ++G + G da+ ++lt++ ++ lcl|FitnessBrowser__Smeli:SMc02878 301 GRLTLADGTLAGADVDMLSSVRFVHQKLGLPIEEAVRMASAYPADAMGIASHKGRLLPGTDADFVLLTPELAMKS 375 *************************************************************************** PP TIGR00221 375 tiveg 379 t + g lcl|FitnessBrowser__Smeli:SMc02878 376 TWIGG 380 98876 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.72 // [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