Align N-acetylglucosamine 6-phosphate deacetylase (NagA;b0677) (EC 3.5.1.25) (characterized)
to candidate 14807 b0677 N-acetylglucosamine-6-phosphate deacetylase (NCBI)
Query= CAZy::AAC73771.1 (382 letters) >FitnessBrowser__Keio:14807 Length = 382 Score = 760 bits (1963), Expect = 0.0 Identities = 382/382 (100%), Positives = 382/382 (100%) Query: 1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQL 60 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQL Sbjct: 1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQL 60 Query: 61 NGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAK 120 NGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAK Sbjct: 61 NGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAK 120 Query: 121 HPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEV 180 HPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEV Sbjct: 121 HPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEV 180 Query: 181 ISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEAD 240 ISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEAD Sbjct: 181 ISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEAD 240 Query: 241 IYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCV 300 IYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCV Sbjct: 241 IYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCV 300 Query: 301 DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANL 360 DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANL Sbjct: 301 DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANL 360 Query: 361 TAFTPDFKITKTIVNGNEVVTQ 382 TAFTPDFKITKTIVNGNEVVTQ Sbjct: 361 TAFTPDFKITKTIVNGNEVVTQ 382 Lambda K H 0.319 0.136 0.396 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: 664 Number of extensions: 7 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: 382 Length of database: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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: 50 (23.9 bits)
Align candidate 14807 b0677 (N-acetylglucosamine-6-phosphate deacetylase (NCBI))
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.23374.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-188 611.7 0.1 2.7e-188 611.5 0.1 1.0 1 lcl|FitnessBrowser__Keio:14807 b0677 N-acetylglucosamine-6-phos Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14807 b0677 N-acetylglucosamine-6-phosphate deacetylase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 611.5 0.1 2.7e-188 2.7e-188 4 380 .] 1 377 [. 1 377 [. 0.99 Alignments for each domain: == domain 1 score: 611.5 bits; conditional E-value: 2.7e-188 TIGR00221 4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnd....asvet 78 +++l++ +i+t++++ldd+avvi+d++ik+v+++ael++ei++++l+g++l+pG+iDvqlnGcgGv++nd svet lcl|FitnessBrowser__Keio:14807 1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDtaeaVSVET 79 69********************************************************************7754456** PP TIGR00221 79 leimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellk 157 leim++a++ksG+t++Lptlit++de +k++v+v+reylak++n ++LGlhleGP+l+l+kkG+h+++++r+pd++l + lcl|FitnessBrowser__Keio:14807 80 LEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPN-QALGLHLEGPWLNLVKKGTHNPNFVRKPDAAL-V 156 ********************************************.********************************.* PP TIGR00221 158 kfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGa 236 +fl+e++dvitkvtlap e+++ae+iskl++agi+vsaGh+nat++e+k++f+aGitfathlynam+++++Repg++Ga lcl|FitnessBrowser__Keio:14807 157 DFLCENADVITKVTLAP-EMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGA 234 *****************.9************************************************************ PP TIGR00221 237 vLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtlaGsslt 315 +Lde+d++++iiaDGlh++++nir+ak+lkgd kl+lvtD++a+aga++e+fifaGk++y+r++ ++d+ngtl+Gsslt lcl|FitnessBrowser__Keio:14807 235 ILDEADIYCGIIADGLHVDYANIRNAKRLKGD-KLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLT 312 ********************************.********************************************** PP TIGR00221 316 miegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltivegk 380 miegv+nlve+++i+l++v+r+++l+para+g+++rlG++a+Gk+anL+++t+df++++tiv+g+ lcl|FitnessBrowser__Keio:14807 313 MIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGN 377 ***************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (382 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: 8.93 // [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