Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_054654192.1 CES79_RS04380 N-acetylglucosamine-6-phosphate deacetylase
Query= BRENDA::Q8Y8E8 (377 letters) >NCBI__GCF_002217945.1:WP_054654192.1 Length = 381 Score = 456 bits (1173), Expect = e-133 Identities = 217/371 (58%), Positives = 273/371 (73%) Query: 5 VITNATIYTGKGVLENAFVRFDKQILEVGSMADFQADKAEEVIDAKGQKLVPGFIDVHSH 64 V+ +ATIYTG+ V+ + ++RFDK I VG M+D+QA ++V G+ +VPGFIDVH+H Sbjct: 4 VLKHATIYTGEEVISDGYIRFDKTIEAVGQMSDYQAQPNDDVKFVNGKVIVPGFIDVHTH 63 Query: 65 GGYSFDAMDADPEALRKQVNGMLNEGITTYFPTTMTQSHENIEKALKVINEVAQTEPVIG 124 GGY FD+MD D + + K VN M+ EGITT FPTTMTQS++NI A+ I E A+ PVI Sbjct: 64 GGYGFDSMDGDADQINKMVNHMVKEGITTVFPTTMTQSNDNIAHAMTGIKEAAKVNPVIK 123 Query: 125 GIHLEGPFVSKVFKGAQPEEYIQAPDLELFKKWFDISGGLIKLVTYAPEHDTSADFENLC 184 G+HLEGPF++ ++KGAQPE+YI+ PD+ L W +SGGL+KL+TYAPE S FE+ C Sbjct: 124 GVHLEGPFIAAIYKGAQPEKYIKDPDVSLLDHWNKLSGGLVKLITYAPEDKGSRVFEDYC 183 Query: 185 FELGVVPSIGHSNDVREHLKTSKATHATHLYNACHRMTHREPGVPGHVLLERGINAELIV 244 +VPS+GHSN R + S+ATH THLYNA HREPGV GH +LE + AELI Sbjct: 184 LSHNIVPSVGHSNATRAQMLASRATHVTHLYNAQREFKHREPGVTGHAMLEENMYAELIC 243 Query: 245 DGIHVHPDMVKLAYQMKGPEHLCIITDSMRAKGMPEGKSELGGQTVIVKDKQARLEDGTL 304 DG H+ PDM+KLAY KGP + ++TDSMRAKGMPEG SELGGQ VIVKDKQARLE G L Sbjct: 244 DGFHIVPDMIKLAYDQKGPHRIELVTDSMRAKGMPEGISELGGQKVIVKDKQARLETGNL 303 Query: 305 AGSVLTYDDGFRNMIKFTGCSVEEAVLMSSGNQAREFNLTQKGAIEAGKDADFNLLDEDL 364 AGSVL YDD FRN++ FTGC +EEAVLM+S NQA EF LTQKG + G DAD N+ D L Sbjct: 304 AGSVLRYDDAFRNVMAFTGCGIEEAVLMTSVNQAEEFGLTQKGKLLPGLDADLNVFDRTL 363 Query: 365 HITATYSFGKK 375 ++ TYS+G++ Sbjct: 364 NLQTTYSYGRE 374 Lambda K H 0.317 0.135 0.391 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: 521 Number of extensions: 22 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: 377 Length of database: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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_054654192.1 CES79_RS04380 (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.2017385.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-93 298.1 0.8 5e-93 298.0 0.8 1.0 1 NCBI__GCF_002217945.1:WP_054654192.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002217945.1:WP_054654192.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.0 0.8 5e-93 5e-93 4 376 .. 2 369 .. 1 373 [. 0.96 Alignments for each domain: == domain 1 score: 298.0 bits; conditional E-value: 5e-93 TIGR00221 4 slllkdkailtendvlddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 s +lk+ +i+t+++v+ d+++ d+ i+av ++ + ++ + ++g v+ pG+iDv+ +G++G d +d NCBI__GCF_002217945.1:WP_054654192.1 2 STVLKHATIYTGEEVISDGYIRF-DKTIEAVGQMSDYQaqPNDDVKFVNGKVIVPGFIDVHTHGGYGFDSMDG 73 57899***************876.899****77665554488888899************************* PP TIGR00221 75 svetleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkey 147 + +++m ++ k+G+t+ pt++t+++++i +a+ ++e+ ++ i G+hleGPf++ kGa+p++y NCBI__GCF_002217945.1:WP_054654192.1 74 DADQINKMVNHMVKEGITTVFPTTMTQSNDNIAHAMTGIKEAAKVNPV--IKGVHLEGPFIAAIYKGAQPEKY 144 ****************************************98777776..99********************* PP TIGR00221 148 irepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathly 220 i++pdv ll ++ + +g++++ +t ape+k+ + + +l ++i+ s+Gh+nat +++ ++ +t++thly NCBI__GCF_002217945.1:WP_054654192.1 145 IKDPDVSLLDHWNKLSGGLVKLITYAPEDKGSRVFEDYCLSHNIVPSVGHSNATRAQMLAS---RATHVTHLY 214 *********************************************************9876...58******* PP TIGR00221 221 namskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGk 293 na +++hRepgv G ++ e+++++e+i DG hi p i+la kg ++ lvtDs++a+g++ + + +G+ NCBI__GCF_002217945.1:WP_054654192.1 215 NAQREFKHREPGVTGHAMLEENMYAELICDGFHIVPDMIKLAYDQKGPHRIELVTDSMRAKGMPEGISELGGQ 287 ************************************************************************* PP TIGR00221 294 evyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavl 366 +v ++++++ + g laGs+l+ ++ +n++ f+++ ++++v ++s n a g+ ++ G + G da+L+v+ NCBI__GCF_002217945.1:WP_054654192.1 288 KVIVKDKQARLETGNLAGSVLRYDDAFRNVMAFTGCGIEEAVLMTSVNQAEEFGLTQK-GKLLPGLDADLNVF 359 ********************************************************99.************** PP TIGR00221 367 tkdfevilti 376 ++ +++ t NCBI__GCF_002217945.1:WP_054654192.1 360 DRTLNLQTTY 369 *****99885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (381 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.49 // [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