Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_009120426.1 BUB52_RS15205 N-acetylglucosamine-6-phosphate deacetylase
Query= BRENDA::Q8Y5F6 (377 letters) >NCBI__GCF_900129655.1:WP_009120426.1 Length = 388 Score = 185 bits (470), Expect = 2e-51 Identities = 105/342 (30%), Positives = 187/342 (54%), Gaps = 20/342 (5%) Query: 45 DGNGRLLIPGMIDVHIHGAKNYDMMDGSTESIQAVSMACAETGCTSFLVTSVSSSLEDLI 104 D G ++PG + +H HG +D + + E+ +++ A G TSF T SS + L Sbjct: 46 DAKGMYIVPGFVCMHAHGGGGHDFNECTEEAFRSIIDAHLAHGATSFYPTISSSPFDKLH 105 Query: 105 QMIRQTKKVIGKEKGAKIAGIHLEGPYLNIEKKGMQNPAHLRHPDLKEMKKIFDEADGLI 164 Q + ++++ E + + G+H+EGPYLN + G Q ++ D +E +++ + + Sbjct: 106 QAAKVCERLMA-EPDSPVLGLHIEGPYLNRKMAGEQFADQVKEIDEQEYRELVESTRCIC 164 Query: 165 KMVTIAPELPGGIELIDFLKKRGVVVAIAHSNATYEEAQDAFEKGASHITHCFNAMPAIH 224 + +PELPG +E +L+++G++ A++H+ A Y+ + A+E G +H H +NAMP H Sbjct: 165 RW-DASPELPGALEFASYLREKGILAAVSHTEAEYDGIRAAYEAGFTHAAHFYNAMPGFH 223 Query: 225 HRA----PGLVAAALENDSISVQAIVDGVHLHPGIVRLIHKIKGPDKMVLTTDAL----- 275 R G V + D ++++ I DG+HL I++L +K+KG + L TDAL Sbjct: 224 KRREYKYEGTVESVYLTDGMTIELIADGIHLPSTILKLAYKLKGVEHTCLVTDALSCAAT 283 Query: 276 QAMGVGDGEYIFGGHQVTVTEGVARLQD-GTLASSTVTMNKSLRLSNEFGINLQDTIQMA 334 + + D YI + +GV +L D +LA S TM+ +R + GI L D ++MA Sbjct: 284 EGKEINDPRYI-------IEDGVCKLADRSSLAGSIATMDVLVRTMAKAGIPLGDALRMA 336 Query: 335 TSTPADILGM-KNLGRIEKGYSADLVLLDKKFEVLSTWINGE 375 + TPA I+G+ G ++K AD++++DK+ + + W G+ Sbjct: 337 SETPARIMGVYDRKGSLQKDKDADILIMDKELNIRAVWQAGK 378 Lambda K H 0.317 0.134 0.380 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: 388 Number of extensions: 22 Number of successful extensions: 6 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: 377 Length of database: 388 Length adjustment: 30 Effective length of query: 347 Effective length of database: 358 Effective search space: 124226 Effective search space used: 124226 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_009120426.1 BUB52_RS15205 (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.3137108.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-80 254.5 0.0 9.1e-80 254.3 0.0 1.0 1 NCBI__GCF_900129655.1:WP_009120426.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900129655.1:WP_009120426.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.3 0.0 9.1e-80 9.1e-80 6 374 .. 4 372 .. 1 378 [. 0.92 Alignments for each domain: == domain 1 score: 254.3 bits; conditional E-value: 9.1e-80 TIGR00221 6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvet 78 +++ +i+t + l+++ v+++d+ki +v+ + + + id+kg ++ pG++ ++ +G+gG+d+n+++ e+ NCBI__GCF_900129655.1:WP_009120426.1 4 QIINGRIFTPQGWLNEGSVLMRDGKILEVTNCDLALIGARLIDAKGMYIVPGFVCMHAHGGGGHDFNECTEEA 76 58899************************9999999************************************* PP TIGR00221 79 leimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirep 151 + + +a +G+tsf pt+ + + +++++a kv+ +a+ ++ +LGlh+eGP+l+ + +G + + ++e+ NCBI__GCF_900129655.1:WP_009120426.1 77 FRSIIDAHLAHGATSFYPTISSSPFDKLHQAAKVCERLMAEPDS-PVLGLHIEGPYLNRKMAGEQFADQVKEI 148 ***99999***************************888877666.**************************** PP TIGR00221 152 dvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynams 224 d + ++++ e++ i + pe+ + e++s l e+gi + + ht+a+y+ +++a++aG t+a h+ynam+ NCBI__GCF_900129655.1:WP_009120426.1 149 DEQEYREL-VESTRCICRWDASPELPGALEFASYLREKGILAAVSHTEAEYDGIRAAYEAGFTHAAHFYNAMP 220 *9997776.57889*********************************************************** PP TIGR00221 225 kld.hRep...gviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGk 293 ++ Re g + +v d+++ e+iaDG+h + ++la klkg +lvtD+l+ a +e +++ NCBI__GCF_900129655.1:WP_009120426.1 221 GFHkRREYkyeGTVESVYLTDGMTIELIADGIHLPSTILKLAYKLKGVEHTCLVTDALSCA--ATEGKEINDP 291 ***666752225666678899************************************9755..5555566766 PP TIGR00221 294 evyiredtlld.kngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLav 365 i+++ + + laGs+ tm v+ + + i+l d++r++s+ par++g+ dr+Gs++k kda++ + NCBI__GCF_900129655.1:WP_009120426.1 292 RYIIEDGVCKLaDRSSLAGSIATMDVLVRTMAKAG-IPLGDALRMASETPARIMGVYDRKGSLQKDKDADILI 363 6667777776646789***************9988.************************************* PP TIGR00221 366 ltkdfevil 374 ++k+ ++ NCBI__GCF_900129655.1:WP_009120426.1 364 MDKELNIRA 372 *****9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (388 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: 27.02 // [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