Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 5208606 Shew_1117 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)
Query= reanno::PV4:5208606 (376 letters) >FitnessBrowser__PV4:5208606 Length = 376 Score = 746 bits (1927), Expect = 0.0 Identities = 376/376 (100%), Positives = 376/376 (100%) Query: 1 MKQTLIAERVFDGEHFHHNQAITIEDGRIVSFDRASDVEPILLAGTLVPGFIDVQVNGGG 60 MKQTLIAERVFDGEHFHHNQAITIEDGRIVSFDRASDVEPILLAGTLVPGFIDVQVNGGG Sbjct: 1 MKQTLIAERVFDGEHFHHNQAITIEDGRIVSFDRASDVEPILLAGTLVPGFIDVQVNGGG 60 Query: 61 GALFNDAPSVEKIKTIGQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTPGVLG 120 GALFNDAPSVEKIKTIGQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTPGVLG Sbjct: 61 GALFNDAPSVEKIKTIGQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTPGVLG 120 Query: 121 IHFEGPHLSVPKKGVHPANYIRRISDEELAVFARNDLGTKVVTLAPENVAPEVIHALVEC 180 IHFEGPHLSVPKKGVHPANYIRRISDEELAVFARNDLGTKVVTLAPENVAPEVIHALVEC Sbjct: 121 IHFEGPHLSVPKKGVHPANYIRRISDEELAVFARNDLGTKVVTLAPENVAPEVIHALVEC 180 Query: 181 GVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAALESQDAWCGLIV 240 GVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAALESQDAWCGLIV Sbjct: 181 GVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAALESQDAWCGLIV 240 Query: 241 DGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDDNASFELFGTQVVRRGDRLNAVTGE 300 DGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDDNASFELFGTQVVRRGDRLNAVTGE Sbjct: 241 DGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDDNASFELFGTQVVRRGDRLNAVTGE 300 Query: 301 LAGCVLDMIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQRGVFTIGARADMVLLGSD 360 LAGCVLDMIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQRGVFTIGARADMVLLGSD Sbjct: 301 LAGCVLDMIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQRGVFTIGARADMVLLGSD 360 Query: 361 NQVARTYIDGQLVYQA 376 NQVARTYIDGQLVYQA Sbjct: 361 NQVARTYIDGQLVYQA 376 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: 649 Number of extensions: 14 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: 376 Length of database: 376 Length adjustment: 30 Effective length of query: 346 Effective length of database: 346 Effective search space: 119716 Effective search space used: 119716 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 5208606 Shew_1117 (N-acetylglucosamine-6-phosphate deacetylase (RefSeq))
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.13882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-94 302.6 0.0 2.2e-94 302.5 0.0 1.0 1 lcl|FitnessBrowser__PV4:5208606 Shew_1117 N-acetylglucosamine-6- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5208606 Shew_1117 N-acetylglucosamine-6-phosphate deacetylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 302.5 0.0 2.2e-94 2.2e-94 6 379 .. 4 370 .. 1 371 [. 0.94 Alignments for each domain: == domain 1 score: 302.5 bits; conditional E-value: 2.2e-94 TIGR00221 6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnd.asvetleim 82 l+ +++ ++ + +++a+ i+d+ i + + +++ i l +l pG+iDvq+nG+gG+ +nd sve ++ + lcl|FitnessBrowser__PV4:5208606 4 TLIAERVFDGEHFHHNQAITIEDGRIVSFDRAS----DVEPILLA-GTLVPGFIDVQVNGGGGALFNDaPSVEKIKTI 76 57788999*****************98765554....45556555.5799******************4466****** PP TIGR00221 83 sealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellkkfl 160 +a a+ G+t+fLptlit e+e ++ a ++ e+la + +LG+h+eGP+ls+ kkG+hp +yir+++ e l f lcl|FitnessBrowser__PV4:5208606 77 GQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTP-GVLGIHFEGPHLSVPKKGVHPANYIRRISDEELAVFA 153 ************************************9988.9**************************9888767776 PP TIGR00221 161 deagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavL 238 + + + vtlap e++ e+i+ l+e g+ v +Gh+na+y+++++a +aG+t thl+nams++d R pg++Ga+L lcl|FitnessBrowser__PV4:5208606 154 RNDLG-TKVVTLAP-ENVAPEVIHALVECGVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAAL 229 66555.5899****.99************************************************************* PP TIGR00221 239 deddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagak.lekfifaGkevyiredtlldkngtlaGsslt 315 +++d +++i+DG+h+hp+ +++a +k k++lvtD++ + g++ +f+ G +v r+d+l g laG +l lcl|FitnessBrowser__PV4:5208606 230 ESQDAWCGLIVDGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDdNASFELFGTQVVRRGDRLNAVTGELAGCVLD 307 ********************************************995679**************************** PP TIGR00221 316 miegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltiveg 379 mi +v n v +++ ++++r+++ +pa +g +r G + G a++++l +d +v +t ++g lcl|FitnessBrowser__PV4:5208606 308 MIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQR-GVFTIGARADMVLLGSDNQVARTYIDG 370 *********************************999.***********************9998 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: 10.21 // [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