Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_025274360.1 HALAL_RS0112695 acetylglutamate kinase
Query= BRENDA::Q6R6P5 (317 letters) >NCBI__GCF_000527155.1:WP_025274360.1 Length = 295 Score = 389 bits (1000), Expect = e-113 Identities = 193/295 (65%), Positives = 233/295 (78%), Gaps = 6/295 (2%) Query: 1 MNDLIKDLGSEVRANVLAEALPWLQHFRDKIVVVKYGGNAMVDDDLKAAFAADMVFLRTV 60 +ND +K +A L EALPWLQ F VVVKYGGNAM+ +L++AFAADMVFLR Sbjct: 5 LNDALK------KAETLVEALPWLQEFHGATVVVKYGGNAMIKPELQSAFAADMVFLRYA 58 Query: 61 GAKPVVVHGGGPQISEMLNRVGLQGEFKGGFRVTTPEVMDIVRMVLFGQVGRDLVGLINS 120 G KPVVVHGGGPQIS ML+++G+ EFKGG RVTTPE D+VRMVL GQVGR+LVGLINS Sbjct: 59 GLKPVVVHGGGPQISAMLDKLGIDSEFKGGLRVTTPEAADVVRMVLVGQVGRELVGLINS 118 Query: 121 HGPYAVGTSGEDAGLFTAQKRMVNIDGVPTDIGLVGDIINVDASSLMDIIEAGRIPVVST 180 HGPYAVG SGEDA +F A++R IDG DIG VGD+ V+ ++ D+I AGRIPV+ST Sbjct: 119 HGPYAVGMSGEDAQMFVAKRRWATIDGEKVDIGRVGDVAGVNTDAVGDLIAAGRIPVIST 178 Query: 181 IAPGEDGQIYNINADTAAGALAAAIGAERLLVLTNVEGLYTDWPDKSSLVSKIKATELEA 240 +A EDG +YN+NADTAAGALAA++ AE+L++LT+VEGLYTDWPDK SLVS+I +L Sbjct: 179 VALDEDGVLYNLNADTAAGALAASLRAEKLVILTDVEGLYTDWPDKDSLVSEINTDDLGG 238 Query: 241 ILPGLDSGMIPKMESCLNAVRGGVSAAHVIDGRIAHSVLLELLTMGGIGTMVLPD 295 +LP L SGMIPKME+CL+AV+GG AAHVIDGRI HS LLE+ T GIGTMV+P+ Sbjct: 239 LLPRLQSGMIPKMEACLHAVKGGTDAAHVIDGRIPHSTLLEVFTHKGIGTMVIPN 293 Lambda K H 0.319 0.139 0.399 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: 352 Number of extensions: 14 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: 317 Length of database: 295 Length adjustment: 27 Effective length of query: 290 Effective length of database: 268 Effective search space: 77720 Effective search space used: 77720 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_025274360.1 HALAL_RS0112695 (acetylglutamate kinase)
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))
# 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.aa/TIGR00761.hmm # target sequence database: /tmp/gapView.17099.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00761 [M=231] Accession: TIGR00761 Description: argB: acetylglutamate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-77 246.4 0.2 1.6e-77 246.2 0.2 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025274360.1 HALAL_RS0112695 acetylglutamate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025274360.1 HALAL_RS0112695 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.2 0.2 1.6e-77 1.6e-77 1 231 [] 29 267 .. 29 267 .. 0.97 Alignments for each domain: == domain 1 score: 246.2 bits; conditional E-value: 1.6e-77 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+V+K+GG+a+ el+ ++a+d+++lr g+k+v+vHGGgp+i+++l+klgi+ ef++glRvT+ e+ lcl|NCBI__GCF_000527155.1:WP_025274360.1 29 TVVVKYGGNAMIkpELQSAFAADMVFLRYAGLKPVVVHGGGPQISAMLDKLGIDSEFKGGLRVTTPEAA 97 69*********999******************************************************* PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltae....kldke..dlgyvGeikkvnkellea 130 +vv+mvl+g+v +elv l++ hg +avG++g+D+q+++a+ ++d e d+g vG++ vn++++ + lcl|NCBI__GCF_000527155.1:WP_025274360.1 98 DVVRMVLVGQVGRELVGLINSHGPYAVGMSGEDAQMFVAKrrwaTIDGEkvDIGRVGDVAGVNTDAVGD 166 ****************************************8887666667799**************** PP TIGR00761 131 llkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliselelee 197 l++ag ipvi+++alde+g l+N+naDtaA++lAa+l AekLv+Ltdv+G++++ dk+sl+se+++++ lcl|NCBI__GCF_000527155.1:WP_025274360.1 167 LIAAGRIPVISTVALDEDGVLYNLNADTAAGALAASLRAEKLVILTDVEGLYTDwpDKDSLVSEINTDD 235 ********************************************************************* PP TIGR00761 198 ieqlikqavikgGmipKveaalealesgvkkvvi 231 + l+ +++GmipK+ea+l+a+++g ++++ lcl|NCBI__GCF_000527155.1:WP_025274360.1 236 LGGLLPR--LQSGMIPKMEACLHAVKGGTDAAHV 267 ******9..7******************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (295 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: 7.53 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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