Align N-acetylglucosamine-6-phosphate deacetylase subunit (EC 3.5.1.25) (characterized)
to candidate WP_019615253.1 G327_RS0113170 N-acetylglucosamine-6-phosphate deacetylase
Query= metacyc::MONOMER-13103 (383 letters) >NCBI__GCF_000381745.1:WP_019615253.1 Length = 382 Score = 266 bits (681), Expect = 6e-76 Identities = 146/375 (38%), Positives = 223/375 (59%), Gaps = 7/375 (1%) Query: 7 ADQFFYPQGIRQGGYLELIDGKFGKLVQSVPQDAEVIDYSGYSIAPGLVDTHIHGFGGVD 66 AD+ F GI + + + +GK + +++P D E+I G S+ PG +D HIHG G D Sbjct: 7 ADRVFGAAGIEKNTAVVVENGKITAVTENIPTDCELIKLEGLSLLPGFIDIHIHGRDGAD 66 Query: 67 VMDNNIEGSLHTMSEGLLTTGVTSFLPTTLTSSYERLLAVTENIGA--RYQEASGAKIRG 124 VMD + + +L +++ L TGV ++ TT+T+ ++ +L + + R ++ GA++ G Sbjct: 67 VMDAS-QSALQNIADALPETGVVGWVGTTVTAPWQDILDSLAAVRSFTRKEQTQGAQLLG 125 Query: 125 LYFEGPYFTEKYKGAQNPAYMKDPSMDEFRAWQKAANGLLNKIALAPERDGVEDFVRTLT 184 + EGPYFTE ++G+ PAY+K P++ E ++AA L + A+APE G + VR LT Sbjct: 126 SFLEGPYFTEPHRGSHPPAYLKSPTISELVELKEAAGSSLIRAAVAPEGTGAMEAVRWLT 185 Query: 185 DEGVTVALGHSNATYDEAKTAVEAGASVWVHAYNGMRGLTHRELGMVGAMYELPH-TYAE 243 + G+ ++ H++AT+++ A GA VH +NGM GL HR+ G GA+ L H AE Sbjct: 186 ENGIKTSVAHTDATFEQVTEAFHLGADCGVHLFNGMSGLHHRQPGCCGAV--LYHDMLAE 243 Query: 244 LICDGHHVDPKACDILLKQKGHENIALITDCMTAGGLEDGDYMLGEFPVVVAEGTARLKS 303 LI DG HV+P + + KG++ IALITDCM AGGL DGDY LG + V +G AR Sbjct: 244 LIADGIHVNPVMMQLAYRMKGYQGIALITDCMRAGGLADGDYQLGAQVITVTDGEAR-SP 302 Query: 304 TGNLAGSILKLKDGLKNVVKWGIANPHQAVMMASLIPAKSVHIDDVCGQIMEGYDADFIV 363 G+LAGS L L+N+V +AV MAS +PAK + I+ G I G DA F + Sbjct: 303 CGSLAGSTCSLDQALRNMVFKSDVPQWEAVQMASAVPAKYLGIEHRLGSIAPGLDASFTI 362 Query: 364 LDKDLELVATYLDGQ 378 +D +L++ T ++G+ Sbjct: 363 MDNELQVQGTIINGE 377 Lambda K H 0.318 0.137 0.406 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: 416 Number of extensions: 28 Number of successful extensions: 5 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: 383 Length of database: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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_019615253.1 G327_RS0113170 (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.3816415.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-99 318.0 0.0 4.6e-99 317.9 0.0 1.0 1 NCBI__GCF_000381745.1:WP_019615253.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_019615253.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 317.9 0.0 4.6e-99 4.6e-99 4 379 .. 2 376 .. 1 377 [. 0.98 Alignments for each domain: == domain 1 score: 317.9 bits; conditional E-value: 4.6e-99 TIGR00221 4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv 76 ++l+ +++ + +++avv++++ki+av+ ++ +++ + i+l+g l+pG+iD++++G G+d++das NCBI__GCF_000381745.1:WP_019615253.1 2 RYALIADRVFGAAGIEKNTAVVVENGKITAVT--ENIPTDCELIKLEGLSLLPGFIDIHIHGRDGADVMDASQ 72 6899999999999999*************996..56789999******************************* PP TIGR00221 77 etleimsealaksGvtsfLptlitredeeikkavkvareylakekn..akiLGlhleGPflslekkGahpkey 147 ++l+ + +al++ Gv++++ t++t++ ++i ++ ++r + ke+ a++LG leGP++ ++G hp+ y NCBI__GCF_000381745.1:WP_019615253.1 73 SALQNIADALPETGVVGWVGTTVTAPWQDILDSLAAVRSFTRKEQTqgAQLLGSFLEGPYFTEPHRGSHPPAY 145 ******************************************998777************************* PP TIGR00221 148 irepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathly 220 ++ p++ l+++ ++ag + + +ape ++ +e ++ l+e+gi s+ ht+at+e+++eaf+ G+ hl+ NCBI__GCF_000381745.1:WP_019615253.1 146 LKSPTISELVELKEAAGSSLIRAAVAPEGTGAMEAVRWLTENGIKTSVAHTDATFEQVTEAFHLGADCGVHLF 218 ******999**************************************************************** PP TIGR00221 221 namskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGk 293 n ms l+hR+pg GavL + d+ +e+iaDG+h++p ++la ++kg + l+tD ++a g+ ++ ++ + + NCBI__GCF_000381745.1:WP_019615253.1 219 NGMSGLHHRQPGCCGAVLYH-DMLAELIADGIHVNPVMMQLAYRMKGYQGIALITDCMRAGGLADGDYQLGAQ 290 ********************.**************************************************** PP TIGR00221 294 evyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavl 366 +++ ++++ g laGs+ + ++++n+v ++++ ++v+++s pa+ lgi++rlGs+a G da +++ NCBI__GCF_000381745.1:WP_019615253.1 291 VITVTDGEARSPCGSLAGSTCSLDQALRNMVFKSDVPQWEAVQMASAVPAKYLGIEHRLGSIAPGLDASFTIM 363 ************************************************************************* PP TIGR00221 367 tkdfeviltiveg 379 +++ +v++ti++g NCBI__GCF_000381745.1:WP_019615253.1 364 DNELQVQGTIING 376 ************9 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.08 // [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