Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate WP_019616715.1 G327_RS0120675 N-acetylglucosamine-6-phosphate deacetylase
Query= CAZy::BAA22834.1 (378 letters) >NCBI__GCF_000381745.1:WP_019616715.1 Length = 377 Score = 483 bits (1244), Expect = e-141 Identities = 231/376 (61%), Positives = 299/376 (79%), Gaps = 1/376 (0%) Query: 1 MYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQL 60 MYALTNC +YT + VL +HAVI+ DKI+ + P++ L + + +DL GANL+PGFIDLQL Sbjct: 1 MYALTNCTVYTTDAVLTEHAVIVEDDKIKNIIPLKQLDAAVEKIDLQGANLTPGFIDLQL 60 Query: 61 NGCGGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPN 120 NGCGGVMFN +TAET+ +M ANLKSGCTS+LPTLITSSDE+M+ A+ R + + N Sbjct: 61 NGCGGVMFNSAVTAETLAVMQTANLKSGCTSYLPTLITSSDEDMKTALQVTRSFINQTEN 120 Query: 121 QSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEK 180 + LGLHLEGPYL++ +KGIH ++IR M+D IC N+D+++KVTLAPEN E +++ Sbjct: 121 EILGLHLEGPYLSIERKGIHRPEYIRKPQTDMVDLICENADIVSKVTLAPENTPIEVVKQ 180 Query: 181 LVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYA 240 L ++GIVVS+GHTNATY++A+ + ++G +FATHLFNAMTPM GRE GV+GA+YD ++YA Sbjct: 181 LSESGIVVSLGHTNATYAQAKAAIDNGASFATHLFNAMTPMTGREAGVIGAVYDN-DIYA 239 Query: 241 GIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDEN 300 GII DGFHV Y N+RI+ KI GEKL+LVTDATAPAGA++D F FVG VYY+DGKC + Sbjct: 240 GIIVDGFHVAYENVRISKKIMGEKLILVTDATAPAGADIDKFDFVGTTVYYKDGKCFGAD 299 Query: 301 GTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVF 360 GTLGGSA+TMIE+++ +V+ VGI L+EA+RMATLYPAKAI V++KLG IK G IANL VF Sbjct: 300 GTLGGSAVTMIESIEQSVKFVGIELEEAVRMATLYPAKAIAVEDKLGSIKPGKIANLAVF 359 Query: 361 DRDFNVKATVVNGQYE 376 D+ V TVVNG Y+ Sbjct: 360 TNDYKVTGTVVNGVYK 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: 467 Number of extensions: 12 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: 378 Length of database: 377 Length adjustment: 30 Effective length of query: 348 Effective length of database: 347 Effective search space: 120756 Effective search space used: 120756 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_019616715.1 G327_RS0120675 (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.3484163.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-155 502.5 6.2 4.1e-155 502.3 6.2 1.0 1 NCBI__GCF_000381745.1:WP_019616715.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_019616715.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.3 6.2 4.1e-155 4.1e-155 4 379 .. 1 372 [. 1 373 [. 0.99 Alignments for each domain: == domain 1 score: 502.3 bits; conditional E-value: 4.1e-155 TIGR00221 4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv 76 +++l++++++t vl ++av+++d+kik++++ ++l+ +++idl+g++ltpG+iD+qlnGcgGv++n a + NCBI__GCF_000381745.1:WP_019616715.1 1 MYALTNCTVYTTDAVLTEHAVIVEDDKIKNIIPLKQLDAAVEKIDLQGANLTPGFIDLQLNGCGGVMFNSAVT 73 69********************************************************************777 PP TIGR00221 77 .etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyi 148 etl +m+ a+ ksG+ts+Lptlit +de++k a++v+r ++++ +n +iLGlhleGP+ls+e+kG+h++eyi NCBI__GCF_000381745.1:WP_019616715.1 74 aETLAVMQTANLKSGCTSYLPTLITSSDEDMKTALQVTRSFINQTEN-EILGLHLEGPYLSIERKGIHRPEYI 145 7**********************************************.************************* PP TIGR00221 149 repdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlyn 221 r+p+ ++ +++++e++d+++kvtlap e++++e++++l e gi+vs+Ghtnaty+++k+a+ G++fathl+n NCBI__GCF_000381745.1:WP_019616715.1 146 RKPQTDM-VDLICENADIVSKVTLAP-ENTPIEVVKQLSESGIVVSLGHTNATYAQAKAAIDNGASFATHLFN 216 *******.******************.99******************************************** PP TIGR00221 222 amskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGke 294 am+++++Re gviGav d+ d++++ii+DG h+ ++n+r+ kk+ g+ kl+lvtD++a+aga+++kf f+G + NCBI__GCF_000381745.1:WP_019616715.1 217 AMTPMTGREAGVIGAVYDN-DIYAGIIVDGFHVAYENVRISKKIMGE-KLILVTDATAPAGADIDKFDFVGTT 287 *****************99.***************************.************************* PP TIGR00221 295 vyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavlt 367 vy+++++++ ++gtl Gs++tmie++ + v fv+i l+++vr+++l+pa+a+ ++d+lGs++ Gk+anLav+t NCBI__GCF_000381745.1:WP_019616715.1 288 VYYKDGKCFGADGTLGGSAVTMIESIEQSVKFVGIELEEAVRMATLYPAKAIAVEDKLGSIKPGKIANLAVFT 360 ************************************************************************* PP TIGR00221 368 kdfeviltiveg 379 +d++v++t+v+g NCBI__GCF_000381745.1:WP_019616715.1 361 NDYKVTGTVVNG 372 **********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (377 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 22.27 // [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