Align succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate 15862 b1744 succinylglutamate desuccinylase (NCBI)
Query= BRENDA::P76215 (322 letters) >FitnessBrowser__Keio:15862 Length = 322 Score = 660 bits (1702), Expect = 0.0 Identities = 322/322 (100%), Positives = 322/322 (100%) Query: 1 MDNFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPV 60 MDNFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPV Sbjct: 1 MDNFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPV 60 Query: 61 EMLDALLGAISHGEIPLRWRLLVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETC 120 EMLDALLGAISHGEIPLRWRLLVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETC Sbjct: 61 EMLDALLGAISHGEIPLRWRLLVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETC 120 Query: 121 RARELEQCLEDFYDQGKESVRWHLDLHTAIRGSLHPQFGVLPQRDIPWDEKFLTWLGAAG 180 RARELEQCLEDFYDQGKESVRWHLDLHTAIRGSLHPQFGVLPQRDIPWDEKFLTWLGAAG Sbjct: 121 RARELEQCLEDFYDQGKESVRWHLDLHTAIRGSLHPQFGVLPQRDIPWDEKFLTWLGAAG 180 Query: 181 LEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSGES 240 LEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSGES Sbjct: 181 LEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSGES 240 Query: 241 VGIVRTPPLRYRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEY 300 VGIVRTPPLRYRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEY Sbjct: 241 VGIVRTPPLRYRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEY 300 Query: 301 VLFPNPLVALGLRAGLMLEKIS 322 VLFPNPLVALGLRAGLMLEKIS Sbjct: 301 VLFPNPLVALGLRAGLMLEKIS 322 Lambda K H 0.322 0.139 0.435 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: 580 Number of extensions: 13 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: 322 Length of database: 322 Length adjustment: 28 Effective length of query: 294 Effective length of database: 294 Effective search space: 86436 Effective search space used: 86436 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate 15862 b1744 (succinylglutamate desuccinylase (NCBI))
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))
# 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/TIGR03242.hmm # target sequence database: /tmp/gapView.22022.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03242 [M=319] Accession: TIGR03242 Description: arg_catab_astE: succinylglutamate desuccinylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-149 481.1 0.0 9.4e-149 480.9 0.0 1.0 1 lcl|FitnessBrowser__Keio:15862 b1744 succinylglutamate desuccin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:15862 b1744 succinylglutamate desuccinylase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 480.9 0.0 9.4e-149 9.4e-149 1 318 [. 3 318 .. 3 319 .. 0.99 Alignments for each domain: == domain 1 score: 480.9 bits; conditional E-value: 9.4e-149 TIGR03242 1 dflaltlekkepevtqgeaknvklrwldeGvlelePeaeaekslvisaGihGnetaPielleqllsdiaagklqlkvrl 79 +flaltl+ k+p++t++e ++v++rwl++Gvlel+P + ++ +lvisaGihGnetaP+e+l++ll +i++g+++l++rl lcl|FitnessBrowser__Keio:15862 3 NFLALTLTGKKPVITEREINGVRWRWLGDGVLELTPLTPPQGALVISAGIHGNETAPVEMLDALLGAISHGEIPLRWRL 81 69***************************************************************************** PP TIGR03242 80 LlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasearyhyDlhtaiRasklekfa 158 L+ilGnp+al++gkRy+++d+nR+fgGr+q ++es e++Ra+eLeq++e+f+++gk+s r+h+DlhtaiR+s++++f+ lcl|FitnessBrowser__Keio:15862 82 LVILGNPPALKQGKRYCHSDMNRMFGGRWQLFAESGETCRARELEQCLEDFYDQGKESV-RWHLDLHTAIRGSLHPQFG 159 **********************************************************8.******************* PP TIGR03242 159 llPyqekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendlsqfqaitealralisd 237 +lP+++ p+d+++l+wl+aa+l+a+++h+e+ggtf+hfs+++++a actlelGka+PfG+ndl+qf+++++a++al+s+ lcl|FitnessBrowser__Keio:15862 160 VLPQRDIPWDEKFLTWLGAAGLEALVFHQEPGGTFTHFSARHFGALACTLELGKALPFGQNDLRQFAVTASAIAALLSG 238 ******************************************************************************* PP TIGR03242 238 eaiparkkeelklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrveeeeerilfPnakvanGlRagl 316 e++++ ++ +l+ ++vv++i+++s+sfe+h+a+d+ nf++f+kGtlla+d +er++v+++ e++lfPn+ va GlRagl lcl|FitnessBrowser__Keio:15862 239 ESVGIVRTPPLR-YRVVSQITRHSPSFEMHMASDTLNFMPFEKGTLLAQDGEERFTVTHDVEYVLFPNPLVALGLRAGL 316 ***********9.****************************************************************** PP TIGR03242 317 ll 318 +l lcl|FitnessBrowser__Keio:15862 317 ML 318 *8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (319 nodes) Target sequences: 1 (322 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: 00:00:00.01 # Mc/sec: 8.98 // [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