Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_110804640.1 C8J30_RS05115 N-acetylglucosamine-6-phosphate deacetylase
Query= reanno::Caulo:CCNA_00452 (378 letters) >NCBI__GCF_003217355.1:WP_110804640.1 Length = 381 Score = 249 bits (635), Expect = 1e-70 Identities = 155/361 (42%), Positives = 209/361 (57%), Gaps = 8/361 (2%) Query: 18 EGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQVNGGGGVLFNDAPTVET 77 +GKAV+++ I ++ A+ P A+ +L GG+L PG ID QVNGGGGV+ + A + Sbjct: 19 DGKAVVLERAQIAAILPASDLPEGARI-ELGGGILAPGLIDLQVNGGGGVMLSGADPLTE 77 Query: 78 IATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPGVLGLHIEGPFLNPKR 137 IATI AAH R GTTG LPTLI+ + + A A+ R VPG LGLH+EGP L+PKR Sbjct: 78 IATICAAHARLGTTGLLPTLITTSSSLTRSVLAAGVAAVGR-VPGFLGLHLEGPHLDPKR 136 Query: 138 KGIHDAGKFRVIDDEALALLTSLKRG--KTLVTLAPERTTPQIIRRLADAGVIVAAGHTN 195 G H A R + ++ L L+ + G ++T+AP TP I RL AGV VA GH + Sbjct: 137 PGCHPAQHIRPMTEDDLDLICEARAGLPALMLTVAPASVTPAQITRLTAAGVTVALGHAD 196 Query: 196 ALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWCGIIVDGRHVDPVVL 255 +A + A G + THLFNAMS L +REPG VGAAL P A G+I DG HV P Sbjct: 197 CSFAEAQAAHAAGASAVTHLFNAMSQLGAREPGLVGAALSLPFA-AGLIADGIHVAPESA 255 Query: 256 KIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVDDHGTLAGSDLDMIGA 315 ++ALR A +R LVTDAM G F+L G+ I + ++ TLAG+DL + A Sbjct: 256 RLALRL-AGERLFLVTDAMAVAGTDLLDFDLAGQRIHRANRSLRTENDTLAGADLSLPEA 314 Query: 316 VRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLCLLNDRLEVAATWIDG 375 +R I++L L + A+ MA+ PA+ +G GR IAP ADL + +V W G Sbjct: 315 IRFCIEVLGLPPEQALAMATARPAALIGSNRGR--IAPSLPADLVHFTEDWQVNRVWQGG 372 Query: 376 Q 376 + Sbjct: 373 K 373 Lambda K H 0.321 0.140 0.410 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: 458 Number of extensions: 18 Number of successful extensions: 7 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: 381 Length adjustment: 30 Effective length of query: 348 Effective length of database: 351 Effective search space: 122148 Effective search space used: 122148 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_110804640.1 C8J30_RS05115 (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.2399875.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-78 249.4 0.0 3.5e-78 249.1 0.0 1.0 1 NCBI__GCF_003217355.1:WP_110804640.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217355.1:WP_110804640.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.1 0.0 3.5e-78 3.5e-78 6 374 .. 5 367 .. 2 373 .. 0.93 Alignments for each domain: == domain 1 score: 249.1 bits; conditional E-value: 3.5e-78 TIGR00221 6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.e 77 +l+ +++ ++ d +avv++ +i a+ + ++l+e+ +i+l g +l+pGliD+q+nG+gGv+ a NCBI__GCF_003217355.1:WP_110804640.1 5 ILTGARLFDGQTCHDGKAVVLERAQIAAILPASDLPEGA-RIELGGGILAPGLIDLQVNGGGGVMLSGADPlT 76 56667788888888999*****************98775.79************************9966558 PP TIGR00221 78 tleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyire 150 + + a a+ G+t+ Lptlit++ ++ + + +++++ ++ LGlhleGP+l +++ G hp ++ir+ NCBI__GCF_003217355.1:WP_110804640.1 77 EIATICAAHARLGTTGLLPTLITTSSSLTRSVLAAGVAAVGRVPG--FLGLHLEGPHLDPKRPGCHPAQHIRP 147 89999999*************************************..************************** PP TIGR00221 151 pdvellkkfldea.gd.vitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlyn 221 + + ++++ea ++ ++t+ap ++t i++l+ ag+ v +Gh++ ++e+++a aG++ +thl+n NCBI__GCF_003217355.1:WP_110804640.1 148 MTEDD-LDLICEArAGlPALMLTVAP-ASVTPAQITRLTAAGVTVALGHADCSFAEAQAAHAAGASAVTHLFN 218 99877.6999998344234567****.7788888899************************************ PP TIGR00221 222 amskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGke 294 ams+l Repg++Ga+L + +++iaDG+h+ p+ +rla +l g+ +l lvtD++a ag++l f aG+ NCBI__GCF_003217355.1:WP_110804640.1 219 AMSQLGAREPGLVGAALSL-PFAAGLIADGIHVAPESARLALRLAGE-RLFLVTDAMAVAGTDLLDFDLAGQR 289 *****************99.9**************************.************************* PP TIGR00221 295 vyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavlt 367 + +++ l +n+tlaG+ l + e+++ +e +++ ++++ +++ pa +g +r G +a a+L+ +t NCBI__GCF_003217355.1:WP_110804640.1 290 IHRANRSLRTENDTLAGADLSLPEAIRFCIEVLGLPPEQALAMATARPAALIGS-NR-GRIAPSLPADLVHFT 360 **************************************************9994.56.*************** PP TIGR00221 368 kdfevil 374 +d++v + NCBI__GCF_003217355.1:WP_110804640.1 361 EDWQVNR 367 ****975 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: 15.48 // [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