Align N-acetylglucosamine 6-phosphate deacetylase (NagA;BSU35010) (EC 3.5.1.25) (characterized)
to candidate WP_010631270.1 RH97_RS05120 N-acetylglucosamine-6-phosphate deacetylase
Query= CAZy::CAB15506.1 (396 letters) >NCBI__GCF_000246965.1:WP_010631270.1 Length = 391 Score = 341 bits (875), Expect = 2e-98 Identities = 183/385 (47%), Positives = 250/385 (64%), Gaps = 3/385 (0%) Query: 11 AIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKEIQAPADSVLLPGMIDIHIHGGYGA 70 +I + ++ I+NG + + GKI V ++P K IQ PA +PGMID+HIHG A Sbjct: 9 SIYSNHDWIENGTLTFDHGKIVGVGHSL-EQPGDKVIQFPAGYKCIPGMIDMHIHGANAA 67 Query: 71 DTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAEESSLLGAEL 130 DTMDA+ L ++S LPEE TTSFLATTITQ I AL NA E ++ AE+ Sbjct: 68 DTMDATHEALSTIASVLPEEATTSFLATTITQSEEAIQAALKNAAEVIGHQKPG--EAEI 125 Query: 131 LGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEEDQHFELIRH 190 LG+HLEGPF+S ++ GAQP+E+I +D E F WQ+ +G I+ VTLAPE ELIRH Sbjct: 126 LGVHLEGPFISKEKCGAQPEEYISDADTERFDNWQKLSGNHIREVTLAPEIKGGMELIRH 185 Query: 191 LKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGTALAHDGFVT 250 L + ++AS+GH++ + A AGA+ +TH+YN M HHREPG++G AL H G T Sbjct: 186 LAAQGVVASIGHSNGYDEDVIRAIDAGATQVTHVYNGMRGMHHREPGILGGALLHHGLYT 245 Query: 251 ELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVTVRGRTALLS 310 ELI DG H LA+ KGS ++ILITD+MRAK LK+G Y+ GGQ V V+ A+LS Sbjct: 246 ELICDGKHVCQGMVNLAYKLKGSDRMILITDAMRAKCLKNGTYDLGGQEVHVKDGLAVLS 305 Query: 311 DGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVTVGKDADLVI 370 GT+AGS+LKM++ R+M FT+ + DI + + N A Q +FDRKGS+ +GKDAD ++ Sbjct: 306 SGTIAGSVLKMDQAFRNMLAFTDATIEDIVQMGAINPALQCNVFDRKGSLEIGKDADFIV 365 Query: 371 VSSDCEVILTICRGNIAFISKEADQ 395 + + ++ LT+CRG IA+ KE Q Sbjct: 366 LDKNNQLALTVCRGEIAYQRKEIVQ 390 Lambda K H 0.316 0.132 0.377 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: 417 Number of extensions: 13 Number of successful extensions: 2 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: 396 Length of database: 391 Length adjustment: 31 Effective length of query: 365 Effective length of database: 360 Effective search space: 131400 Effective search space used: 131400 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_010631270.1 RH97_RS05120 (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.2173177.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-117 377.2 4.1 4.8e-117 377.0 4.1 1.0 1 NCBI__GCF_000246965.1:WP_010631270.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000246965.1:WP_010631270.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 377.0 4.1 4.8e-117 4.8e-117 8 379 .. 6 379 .. 1 380 [. 0.97 Alignments for each domain: == domain 1 score: 377.0 bits; conditional E-value: 4.8e-117 TIGR00221 8 kdkailtendvlddsavvindekikavvteaeleeeikeidlkg.nvltpGliDvqlnGcgGvdtndasvetl 79 ++i+ ++d ++++ + +ki v + e +++ k i+ ++ pG+iD++++G++ +dt+da+ e+l NCBI__GCF_000246965.1:WP_010631270.1 6 VGCSIYSNHDWIENGTLTFDHGKIVGVGHSLE-QPGDKVIQFPAgYKCIPGMIDMHIHGANAADTMDATHEAL 77 5699*********************9987766.5788999999857799************************ PP TIGR00221 80 eimsealaksGvtsfLptlitredeeikkavkvareylakekn..akiLGlhleGPflslekkGahpkeyire 150 + + l+++ +tsfL+t+it+++e i+ a+k+a e ++ +k a+iLG+hleGPf+s ek Ga+p+eyi + NCBI__GCF_000246965.1:WP_010631270.1 78 STIASVLPEEATTSFLATTITQSEEAIQAALKNAAEVIGHQKPgeAEILGVHLEGPFISKEKCGAQPEEYISD 150 ***************************************998778**************************** PP TIGR00221 151 pdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynam 223 +d e + ++++ +g++i+ vtlape k+ +eli++l+ +g+++s+Gh+n e ++ a+ aG+t +th+yn m NCBI__GCF_000246965.1:WP_010631270.1 151 ADTERFDNWQKLSGNHIREVTLAPEIKGGMELIRHLAAQGVVASIGHSNGYDEDVIRAIDAGATQVTHVYNGM 223 ************************************************************************* PP TIGR00221 224 skldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevy 296 ++hRepg++G +L + +++te+i DG h+ + la klkg+ +++l+tD+++a+++k +++ +G+ev NCBI__GCF_000246965.1:WP_010631270.1 224 RGMHHREPGILGGALLHHGLYTELICDGKHVCQGMVNLAYKLKGSDRMILITDAMRAKCLKNGTYDLGGQEVH 296 ************************************************************************* PP TIGR00221 297 iredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkd 369 ++++ ++ ++gt+aGs+l+m ++ +n++ f++ +++d+v++ + npa + +++dr+Gs++ Gkda+ vl+k+ NCBI__GCF_000246965.1:WP_010631270.1 297 VKDGLAVLSSGTIAGSVLKMDQAFRNMLAFTDATIEDIVQMGAINPALQCNVFDRKGSLEIGKDADFIVLDKN 369 ************************************************************************* PP TIGR00221 370 feviltiveg 379 ++ lt+++g NCBI__GCF_000246965.1:WP_010631270.1 370 NQLALTVCRG 379 ********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (391 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: 16.81 // [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