Align N-succinylglutamate kinase (EC 2.7.2.-) (characterized)
to candidate Echvi_3850 Echvi_3850 acetylglutamate kinase
Query= reanno::Btheta:352922 (257 letters) >FitnessBrowser__Cola:Echvi_3850 Length = 266 Score = 264 bits (675), Expect = 1e-75 Identities = 129/236 (54%), Positives = 173/236 (73%) Query: 4 KLTVIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVNGRR 63 K++++K+GG ++++ A L + L FA + G K+LVHGGG A+K QLGIE KMV+GRR Sbjct: 2 KISIVKIGGNVIDDPAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDGRR 61 Query: 64 ITDAETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPVKEVDYGFVG 123 ITD TL VVTMVY G++NK IVA LQ NA+G TGAD N+IRS KRPVK++DYGFVG Sbjct: 62 ITDEATLDVVTMVYAGMINKKIVAKLQQLEQNAMGFTGADGNLIRSAKRPVKDIDYGFVG 121 Query: 124 DVEKVDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAGETAKALSALFDVTLVYC 183 DV++VD L+ L+ K VVPV + +THD +GN+LNTNADTIA E A A++ V L +C Sbjct: 122 DVKEVDTELMEVLLEKDVVPVFSAITHDRKGNLLNTNADTIASEIATAMAVKHTVRLYFC 181 Query: 184 FEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLENSFEAINAGVTEV 239 F K GVL DE++DDS++P+I +++ D VI GMIPKL+N+F A++ GV+ V Sbjct: 182 FNKAGVLIDEHNDDSLVPKINEDIYDELKRDNVIHSGMIPKLDNAFSALHKGVSNV 237 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: 232 Number of extensions: 9 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: 257 Length of database: 266 Length adjustment: 25 Effective length of query: 232 Effective length of database: 241 Effective search space: 55912 Effective search space used: 55912 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 Echvi_3850 Echvi_3850 (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.14270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-62 195.8 2.1 4.5e-62 195.6 2.1 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3850 Echvi_3850 acetylglutamate kinas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3850 Echvi_3850 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 195.6 2.1 4.5e-62 4.5e-62 3 229 .. 5 237 .. 3 239 .. 0.91 Alignments for each domain: == domain 1 score: 195.6 bits; conditional E-value: 4.5e-62 TIGR00761 3 ViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 ++KiGG++i++ +l + ++ ++ + k ++vHGGg + ++ ++lgie+++v+g R+Td++tl+vv+mv++g lcl|FitnessBrowser__Cola:Echvi_3850 5 IVKIGGNVIDD-PAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDGRRITDEATLDVVTMVYAG 77 8*********7.566666666666666666******************************************** PP TIGR00761 77 kvnkelvallekhgikavGltgkDgqlltae..kldkedlgyvGeikkvnkelleallkagiipviaslaldee 148 +nk++va+l++ + +a+G tg+Dg+l+ +++ d+g+vG++k+v++el+e ll+++++pv +++ d + lcl|FitnessBrowser__Cola:Echvi_3850 78 MINKKIVAKLQQLEQNAMGFTGADGNLIRSAkrPVKDIDYGFVGDVKEVDTELMEVLLEKDVVPVFSAITHDRK 151 ****************************98844455559*********************************** PP TIGR00761 149 gqllNvnaDtaAaelAaaleAe...kLvlLtdvaGileg..dkksliseleleeieqlikqavikgGmipKvea 217 g+llN+naDt+A+e+A+a+ + +L++ ++aG+l + + +sl+ +++ + +++l + +vi++GmipK+++ lcl|FitnessBrowser__Cola:Echvi_3850 152 GNLLNTNADTIASEIATAMAVKhtvRLYFCFNKAGVLIDehNDDSLVPKINEDIYDELKRDNVIHSGMIPKLDN 225 *******************76633379999******988787888***************************** PP TIGR00761 218 alealesgvkkv 229 a +al++gv++v lcl|FitnessBrowser__Cola:Echvi_3850 226 AFSALHKGVSNV 237 *********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (266 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: 8.61 // [ok]
This GapMind analysis is from Apr 09 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