Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate WP_033298634.1 G327_RS0118820 N-acetylglucosamine-6-phosphate deacetylase
Query= CAZy::BAA22834.1 (378 letters) >NCBI__GCF_000381745.1:WP_033298634.1 Length = 379 Score = 308 bits (789), Expect = 2e-88 Identities = 158/374 (42%), Positives = 232/374 (62%), Gaps = 4/374 (1%) Query: 2 YALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNV-VDLNGANLSPGFIDLQL 60 +ALTN ++ G+ VL ++I G I++V P+ES+ S + + G + GFIDLQL Sbjct: 5 FALTNVDVFDGDKVLNNQVIVIEGQTIKSVAPMESVTSLPEIQIASPGLLATAGFIDLQL 64 Query: 61 NGCGGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPN 120 NGCGGV+ N I +T+ +M+ NL SG T +LPTL+TSS ++ +A+ + Sbjct: 65 NGCGGVLLNSAIEEKTLTVMNHTNLISGTTQYLPTLVTSSQADLCKAVELVEGLKNPEEQ 124 Query: 121 QSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEK 180 LGLHLEGP++N KKG H+ +IR D D + + + +T+APE E I K Sbjct: 125 GILGLHLEGPFINKKKKGAHAQQYIRELDTAAADYLTEHKSAVKVLTVAPECVSQEVINK 184 Query: 181 LVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYA 240 L AGI+VS+GHTNATY + + GI ATHL+NAMTP+ REPG VG + + Y+ Sbjct: 185 LTSAGIIVSMGHTNATYEQLEN--KQGIVMATHLYNAMTPLTSREPGAVGYVLN-HRPYS 241 Query: 241 GIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDEN 300 GII DG H D+A +R+AH+ GE+L +VTDA PAG ++ F G + GKC + Sbjct: 242 GIIVDGIHSDFAAVRLAHEHLGERLFMVTDAVTPAGTDLTEFDMAGTAAFVSQGKCHFAD 301 Query: 301 GTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVF 360 GT+ G+++TMI+ + N ++ VG++ +EALRMA+LYPA+A+ + + GRIK G AN+T+ Sbjct: 302 GTIAGASITMIKGIHNLIDKVGLSREEALRMASLYPAQAVNMAHQYGRIKAGYKANITLL 361 Query: 361 DRDFNVKATVVNGQ 374 + D V + G+ Sbjct: 362 NADNEVNSVYQMGR 375 Lambda K H 0.318 0.135 0.388 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: 362 Number of extensions: 11 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: 379 Length adjustment: 30 Effective length of query: 348 Effective length of database: 349 Effective search space: 121452 Effective search space used: 121452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_033298634.1 G327_RS0118820 (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.3446755.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-108 348.8 4.1 2.1e-108 348.6 4.1 1.0 1 NCBI__GCF_000381745.1:WP_033298634.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_033298634.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.6 4.1 2.1e-108 2.1e-108 4 373 .. 4 368 .. 1 374 [. 0.97 Alignments for each domain: == domain 1 score: 348.6 bits; conditional E-value: 2.1e-108 TIGR00221 4 slllkdkailtendvlddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 ++l+++ ++ + vl+++ +vi+++ ik+v + + +ei +i +g t+G+iD+qlnGcgGv n a NCBI__GCF_000381745.1:WP_033298634.1 4 AFALTNVDVFDGDKVLNNQVIVIEGQTIKSVAPMESVTslPEI-QIASPGLLATAGFIDLQLNGCGGVLLNSA 75 5799*****************************9999855565.578899999******************98 PP TIGR00221 75 sv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpke 146 +tl +m++++ sG+t++Lptl+t ++ ++ kav+ + ++ e++ iLGlhleGPf++ +kkGah ++ NCBI__GCF_000381745.1:WP_033298634.1 76 IEeKTLTVMNHTNLISGTTQYLPTLVTSSQADLCKAVELVEGLKNPEEQ-GILGLHLEGPFINKKKKGAHAQQ 147 7769*****************************************9999.9********************** PP TIGR00221 147 yirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathl 219 yire d + ++l+e ++ +t+ap e + e+i+kl+ agiivs+Ghtnatye+l++ k+Gi athl NCBI__GCF_000381745.1:WP_033298634.1 148 YIRELDTAA-ADYLTEHKSAVKVLTVAP-ECVSQEVINKLTSAGIIVSMGHTNATYEQLEN--KQGIVMATHL 216 ********9.******************.999***************************86..89******** PP TIGR00221 220 ynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaG 292 ynam++l+ Repg++G vL++ +++ii+DG+h++++++rla+ g+ +l +vtD++++ag++l +f +aG NCBI__GCF_000381745.1:WP_033298634.1 217 YNAMTPLTSREPGAVGYVLNH-RPYSGIIVDGIHSDFAAVRLAHEHLGE-RLFMVTDAVTPAGTDLTEFDMAG 287 *********************.889************************.*********************** PP TIGR00221 293 kevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLav 365 ++ ++++ ++gt+aG+s+tmi+g++nl++ v++s ++++r++sl+pa+a+++ ++ G +++G+ an+++ NCBI__GCF_000381745.1:WP_033298634.1 288 TAAFVSQGKCHFADGTIAGASITMIKGIHNLIDKVGLSREEALRMASLYPAQAVNMAHQYGRIKAGYKANITL 360 ************************************************************************* PP TIGR00221 366 ltkdfevi 373 l+ d ev NCBI__GCF_000381745.1:WP_033298634.1 361 LNADNEVN 368 ****9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (379 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 16.04 // [ok]
This GapMind analysis is from Sep 24 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