Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 202606 SO3505 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)
Query= reanno::MR1:202606 (378 letters) >FitnessBrowser__MR1:202606 Length = 378 Score = 745 bits (1924), Expect = 0.0 Identities = 378/378 (100%), Positives = 378/378 (100%) Query: 1 MKFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTALGAKEVRYTGTLVPGFIDVQVNGGG 60 MKFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTALGAKEVRYTGTLVPGFIDVQVNGGG Sbjct: 1 MKFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTALGAKEVRYTGTLVPGFIDVQVNGGG 60 Query: 61 GALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAGVLG 120 GALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAGVLG Sbjct: 61 GALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAGVLG 120 Query: 121 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES 180 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES Sbjct: 121 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES 180 Query: 181 GVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV 240 GVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV Sbjct: 181 GVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV 240 Query: 241 DGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300 DGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE Sbjct: 241 DGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300 Query: 301 LAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDN 360 LAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDN Sbjct: 301 LAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDN 360 Query: 361 QYQVLANYIAGNAVYVRP 378 QYQVLANYIAGNAVYVRP Sbjct: 361 QYQVLANYIAGNAVYVRP 378 Lambda K H 0.321 0.137 0.400 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: 634 Number of extensions: 18 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: 378 Length of database: 378 Length adjustment: 30 Effective length of query: 348 Effective length of database: 348 Effective search space: 121104 Effective search space used: 121104 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 202606 SO3505 (N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file))
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.22751.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-95 306.4 0.0 1.6e-95 306.2 0.0 1.0 1 lcl|FitnessBrowser__MR1:202606 SO3505 N-acetylglucosamine-6-pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:202606 SO3505 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 306.2 0.0 1.6e-95 1.6e-95 5 380 .] 3 372 .. 1 372 [. 0.92 Alignments for each domain: == domain 1 score: 306.2 bits; conditional E-value: 1.6e-95 TIGR00221 5 lllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etleim 82 + l+ +++ ++ + +d v i+d++i + t + ke+ g +l pG+iDvq+nG+gG+ +n + +e + lcl|FitnessBrowser__MR1:202606 3 FTLIAEQLFDGESFHQDVPVTIEDGLIASFDTAL----GAKEVRYTG-TLVPGFIDVQVNGGGGALFNTSPTvACIETI 76 566777888899999999********99987764....455566555.699*****************96554****** PP TIGR00221 83 sealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellkkfld 161 +a a+ G+t+fLptlit + + + ka ++ ++a +k+a +LG+h+eGP+ls+ kkG+hp+ +ire++ + l + + lcl|FitnessBrowser__MR1:202606 77 GKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVA-QKSAGVLGVHFEGPHLSVPKKGVHPQGFIREITEAEL-AIFC 153 ***************************998876665.5677***************************986553.5666 PP TIGR00221 162 eagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLde 240 i+ vtlap e++ e+i+ l+e g+ v +Gh+na+y+++ +a kaG+t thlynams+l Repgv+Ga++++ lcl|FitnessBrowser__MR1:202606 154 RQDLGIRVVTLAP-ENVSPEVIRLLVESGVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIES 231 67777********.99*************************************************************** PP TIGR00221 241 ddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagakle.kfifaGkevyiredtlldkngtlaGssltmie 318 + +++i+DG+h+hp+++r+a ++k k++lvtD++ + g+++e +f+ G +v +d+l g laG +l m lcl|FitnessBrowser__MR1:202606 232 ETAWCGLIVDGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDEtSFELFGTQVLRVGDRLNAVTGELAGCVLDMAS 310 *******************************************96538******************************* PP TIGR00221 319 gvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltivegk 380 +v+n v+ +++l +++r+++l+pa lgi d G +a+G+ a+L++l+++++v + g+ lcl|FitnessBrowser__MR1:202606 311 AVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDNQYQVLANYIAGN 372 ******************************************************98888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (378 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.00 // [ok]
This GapMind analysis is from Sep 17 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