Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate HSERO_RS22760 HSERO_RS22760 N-acetylglucosamine-6-phosphate deacetylase
Query= reanno::BFirm:BPHYT_RS02730 (367 letters) >FitnessBrowser__HerbieS:HSERO_RS22760 Length = 375 Score = 475 bits (1223), Expect = e-139 Identities = 236/365 (64%), Positives = 287/365 (78%), Gaps = 4/365 (1%) Query: 2 LTGNILTTDGWIHGTLEYENGRITALTGE--RADPSTND-APYILPGFIDLHVHGGGGSD 58 L GN+LT GW HG++ ++ RI ++ G R +P D YILPGFIDLHVHGGGG D Sbjct: 7 LHGNVLTPQGWTHGSMVFDQ-RIRSIDGRPLRREPRLIDEGDYILPGFIDLHVHGGGGRD 65 Query: 59 VMEGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVH 118 VMEGG A++ + R HAR+GTTSLLATTMTAP EL + + + R PG ARVLGVH Sbjct: 66 VMEGGDAVQVLARLHARHGTTSLLATTMTAPLAELEVALKAIRTSTDTRPPGHARVLGVH 125 Query: 119 LEGPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVR 178 LEGPYINPGKLGAQPD A+ A +++V S+APIR++T+APE+ GH++++ ++A RG++ Sbjct: 126 LEGPYINPGKLGAQPDFAIEASLEQVDHLNSLAPIRLITIAPEVDGHLKLVCKLAHRGMK 185 Query: 179 VQLGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLH 238 VQ+GH+ G+YDD VAAL HGA GFTHLFNAMS HHR PG+VGAALAHA++AE+IPDLLH Sbjct: 186 VQIGHTDGSYDDGVAALAHGASGFTHLFNAMSGFHHRAPGMVGAALAHAQYAELIPDLLH 245 Query: 239 VHPGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLT 298 VHPGAIRAALR+IPRL+ VTDST+A GMPDG+Y LG Q V KC GGVRL DGTLAGS LT Sbjct: 246 VHPGAIRAALRSIPRLFCVTDSTAAAGMPDGDYALGRQVVHKCAGGVRLDDGTLAGSILT 305 Query: 299 MDQALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYV 358 MDQALRNL+S+G+ +A+ S R S YAADYLG+ DRGR+A G ADVVV DR+ AL A YV Sbjct: 306 MDQALRNLISLGMDVAEASLRTSTYAADYLGLADRGRLATGCHADVVVLDRQFALKAVYV 365 Query: 359 EGEAI 363 EGE I Sbjct: 366 EGEEI 370 Lambda K H 0.319 0.136 0.399 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: 481 Number of extensions: 19 Number of successful extensions: 2 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: 367 Length of database: 375 Length adjustment: 30 Effective length of query: 337 Effective length of database: 345 Effective search space: 116265 Effective search space used: 116265 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate HSERO_RS22760 HSERO_RS22760 (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.5552.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-78 250.9 0.0 1.2e-78 250.6 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS22760 HSERO_RS22760 N-acetylglucosamin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS22760 HSERO_RS22760 N-acetylglucosamine-6-phosphate deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.6 0.0 1.2e-78 1.2e-78 38 379 .. 34 367 .. 18 368 .. 0.92 Alignments for each domain: == domain 1 score: 250.6 bits; conditional E-value: 1.2e-78 TIGR00221 38 aeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredee 105 ++l+ e + id +g +++pG+iD++++G+gG d+++ ++++++ + a++G+ts L+t++t++ e lcl|FitnessBrowser__HerbieS:HSERO_RS22760 34 RPLRREPRLID-EGDYILPGFIDLHVHGGGGRDVMEG-GDAVQVLARLHARHGTTSLLATTMTAPLAE 99 55666666666.799*******************975.5899999999******************** PP TIGR00221 106 ikkavkvareylakekn..akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvt 171 ++ a+k++r + a++LG+hleGP++++ k Ga+p ++ e++ e ++ l+ + i+ +t lcl|FitnessBrowser__HerbieS:HSERO_RS22760 100 LEVALKAIRTSTDTRPPghARVLGVHLEGPYINPGKLGAQP-DFAIEASLEQ-VDHLNSLA-PIRLIT 164 **********999887668********************97.6777888888.67777655.69**** PP TIGR00221 172 lapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLd 239 +ape +++ +l+ kl++ g+ v++Ght+ y+ +a G++ thl+nams ++hR pg++Ga+L+ lcl|FitnessBrowser__HerbieS:HSERO_RS22760 165 IAPEVDGHLKLVCKLAHRGMKVQIGHTDGSYDDGVAALAHGASGFTHLFNAMSGFHHRAPGMVGAALA 232 ******************************************************************** PP TIGR00221 240 eddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkng 307 + ++e+i D lh+hp +ir a l+ + +l vtDs+aaag++++ + + + v +++ ++g lcl|FitnessBrowser__HerbieS:HSERO_RS22760 233 H-AQYAELIPDLLHVHPGAIRAA--LRSIPRLFCVTDSTAAAGMPDGDYALGRQVVHKCAGGVRLDDG 297 *.679****************97..567888******************9999999999999999*** PP TIGR00221 308 tlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevilt 375 tlaGs+ltm ++++nl+ + + ++++ +s ++a lg+ dr G +a+G a+++vl+++f ++ lcl|FitnessBrowser__HerbieS:HSERO_RS22760 298 TLAGSILTMDQALRNLISLG-MDVAEASLRTSTYAADYLGLADR-GRLATGCHADVVVLDRQFALKAV 363 ******************99.***********************.*********************99 PP TIGR00221 376 iveg 379 veg lcl|FitnessBrowser__HerbieS:HSERO_RS22760 364 YVEG 367 9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (375 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: 7.58 // [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