Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_013553363.1 NITSA_RS02030 acetylglutamate kinase
Query= BRENDA::Q6V1L5 (301 letters) >NCBI__GCF_000186245.1:WP_013553363.1 Length = 283 Score = 263 bits (671), Expect = 5e-75 Identities = 134/277 (48%), Positives = 183/277 (66%), Gaps = 5/277 (1%) Query: 14 VRILSEALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGGPE 73 V+ L EALPY+++F +V+KYGG+A + EELK +DIV L VGMRPVVVHGGG Sbjct: 8 VQTLLEALPYIKKFRDEIIVIKYGGSAQESEELKAKFAQDIVLLHTVGMRPVVVHGGGKN 67 Query: 74 INAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGGRAVGFCGTDG 133 I L +G++ +F +G RVT + M V EMVL G +NK+IV+ +N+ G RAVG G D Sbjct: 68 ITRLLSDLGVDTRFIDGQRVTTREVMRVAEMVLSGEINKEIVALLNSQGARAVGISGKDA 127 Query: 134 RLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADE--NGQSFNINADTV 191 + A P D E G+ G + +N+E+++ +L+ G++PVI+ +A + FNINAD Sbjct: 128 NFLEAIPKDSENFGYTGVIEQINTEIVDNILDDGFVPVIAPIAGSQTLGHPGFNINADLA 187 Query: 192 AGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGGGMIPKVDC 251 A IA AL A K++ LTDT G+L+ + LIP L I Q+R L + ++ GGMIPKVD Sbjct: 188 ASRIAVALGARKILFLTDTPGVLDGEGK---LIPTLTIDQTRRLKEEEVIRGGMIPKVDA 244 Query: 252 CIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMI 288 CI +L GV+ AHIIDGR+ H+LLLEI T +GIGT I Sbjct: 245 CIDALRGGVKKAHIIDGRVEHSLLLEILTSSGIGTCI 281 Lambda K H 0.320 0.139 0.406 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: 265 Number of extensions: 15 Number of successful extensions: 3 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: 301 Length of database: 283 Length adjustment: 26 Effective length of query: 275 Effective length of database: 257 Effective search space: 70675 Effective search space used: 70675 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: 48 (23.1 bits)
Align candidate WP_013553363.1 NITSA_RS02030 (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.13960.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-80 255.1 1.1 3.4e-80 254.9 1.1 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553363.1 NITSA_RS02030 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553363.1 NITSA_RS02030 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.9 1.1 3.4e-80 3.4e-80 2 231 .] 26 258 .. 25 258 .. 0.97 Alignments for each domain: == domain 1 score: 254.9 bits; conditional E-value: 3.4e-80 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketle 68 iViK+GG+a + el+ ++a+di+ l+ +g+++v+vHGGg++i++ll+ lg++++f++g+RvT++e++ lcl|NCBI__GCF_000186245.1:WP_013553363.1 26 IVIKYGGSAQEseELKAKFAQDIVLLHTVGMRPVVVHGGGKNITRLLSDLGVDTRFIDGQRVTTREVMR 94 9*******998889******************************************************* PP TIGR00761 69 vvemvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagii 137 v+emvl g++nke+vall+ +g++avG++gkD++ l+a d+e+ gy+G+i+++n+e+++++l+ g++ lcl|NCBI__GCF_000186245.1:WP_013553363.1 95 VAEMVLSGEINKEIVALLNSQGARAVGISGKDANFLEAIPKDSENFGYTGVIEQINTEIVDNILDDGFV 163 ********************************************************************* PP TIGR00761 138 pviaslald..eegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikq 204 pvia++a + + +N+naD aA+ +A al+A k+++Ltd++G+l+g + +li l++++ ++l ++ lcl|NCBI__GCF_000186245.1:WP_013553363.1 164 PVIAPIAGSqtLGHPGFNINADLAASRIAVALGARKILFLTDTPGVLDG-EGKLIPTLTIDQTRRLKEE 231 *******8842456779********************************.666**************** PP TIGR00761 205 avikgGmipKveaalealesgvkkvvi 231 +vi+gGmipKv+a+++al++gvkk++i lcl|NCBI__GCF_000186245.1:WP_013553363.1 232 EVIRGGMIPKVDACIDALRGGVKKAHI 258 *************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (283 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: 8.63 // [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