Align N-succinylglutamate kinase (EC 2.7.2.-) (characterized)
to candidate WP_101442813.1 BD749_RS02620 acetylglutamate kinase
Query= reanno::Btheta:352922 (257 letters) >NCBI__GCF_002846395.1:WP_101442813.1 Length = 265 Score = 265 bits (676), Expect = 9e-76 Identities = 134/250 (53%), Positives = 177/250 (70%), Gaps = 3/250 (1%) Query: 7 VIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVNGRRITD 66 +IK+GG ++++ L + L DFA +SG K+LVHGGG+ A+ I +LGI V GRR+TD Sbjct: 3 IIKIGGNVLDKPERLQRFLIDFAQLSGLKLLVHGGGKIASTIGLRLGIAPAYVEGRRLTD 62 Query: 67 AETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPVKEVDYGFVGDV- 125 AETL+VVTMVYGGL+NKN+VA LQA G NA+G+TGAD N I + KRPVK VDYG+ GD+ Sbjct: 63 AETLQVVTMVYGGLINKNVVAQLQALGCNAIGMTGADANAIPATKRPVKTVDYGYAGDIA 122 Query: 126 --EKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAGETAKALSALFDVTLVYC 183 E ++A+ + L+ G+ PV APLTHDG GNMLNTNADTIA A AL+ ++V LVYC Sbjct: 123 GPETINATAIRALLSAGLTPVFAPLTHDGHGNMLNTNADTIASVLATALAPHYNVQLVYC 182 Query: 184 FEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEVVITL 243 FEKKGVL D +DD+SVI I +++ G++ GMIPKL+N+F A+ GV V+I Sbjct: 183 FEKKGVLADASDDNSVISHIDENRYKELKEKGIVTDGMIPKLDNAFAALRQGVKAVLIGE 242 Query: 244 ASAIKDNEGT 253 A + G+ Sbjct: 243 AEGLASLAGS 252 Lambda K H 0.316 0.135 0.366 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: 247 Number of extensions: 9 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: 257 Length of database: 265 Length adjustment: 25 Effective length of query: 232 Effective length of database: 240 Effective search space: 55680 Effective search space used: 55680 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_101442813.1 BD749_RS02620 (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.3185176.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-59 186.1 0.6 4.1e-59 185.9 0.6 1.0 1 NCBI__GCF_002846395.1:WP_101442813.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101442813.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 185.9 0.6 4.1e-59 4.1e-59 1 231 [] 1 240 [. 1 240 [. 0.91 Alignments for each domain: == domain 1 score: 185.9 bits; conditional E-value: 4.1e-59 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 + +iKiGG++++ e l++++ d a+ +g+k ++vHGGg+ +++ +lgi + +v+g R+Td+etl+vv+ NCBI__GCF_002846395.1:WP_101442813.1 1 MYIIKIGGNVLDkpERLQRFLIDFAQ--LSGLK-LLVHGGGKIASTIGLRLGIAPAYVEGRRLTDAETLQVVT 70 679*********44444555444444..45677.89************************************* PP TIGR00761 72 mvligkvnkelvallekhgikavGltgkDgqlltae..kldkedlgyvGei...kkvnkelleallkagiipv 139 mv+ g +nk++va+l+ g++a+G+tg+D++ + a+ ++ d+gy G+i + +n+ +++all ag +pv NCBI__GCF_002846395.1:WP_101442813.1 71 MVYGGLINKNVVAQLQALGCNAIGMTGADANAIPATkrPVKTVDYGYAGDIagpETINATAIRALLSAGLTPV 143 ***********************************955455559*****9855579***************** PP TIGR00761 140 iaslaldeegqllNvnaDtaAaelAaaleAe...kLvlLtdvaGileg..dkksliseleleeieqlikqavi 207 a+l d +g++lN+naDt+A+ lA+al ++ +Lv+ +++G+l++ d +s+is+++ +++++l +++++ NCBI__GCF_002846395.1:WP_101442813.1 144 FAPLTHDGHGNMLNTNADTIASVLATALAPHynvQLVYCFEKKGVLADasDDNSVISHIDENRYKELKEKGIV 216 ****************************9875557************9999999******************* PP TIGR00761 208 kgGmipKveaalealesgvkkvvi 231 ++GmipK+++a +al++gvk+v i NCBI__GCF_002846395.1:WP_101442813.1 217 TDGMIPKLDNAFAALRQGVKAVLI 240 ********************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (265 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 23.09 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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