Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 17978 b3939 cystathionine gamma-synthase (NCBI)
Query= SwissProt::P00935 (386 letters) >FitnessBrowser__Keio:17978 Length = 386 Score = 764 bits (1972), Expect = 0.0 Identities = 386/386 (100%), Positives = 386/386 (100%) Query: 1 MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60 MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA Sbjct: 1 MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60 Query: 61 LAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL 120 LAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL Sbjct: 61 LAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL 120 Query: 121 FVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPA 180 FVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPA Sbjct: 121 FVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPA 180 Query: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYL 240 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYL Sbjct: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYL 240 Query: 241 LLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300 LLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML Sbjct: 241 LLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300 Query: 301 SFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360 SFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL Sbjct: 301 SFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360 Query: 361 RISTGIEDGEDLIADLENGFRAANKG 386 RISTGIEDGEDLIADLENGFRAANKG Sbjct: 361 RISTGIEDGEDLIADLENGFRAANKG 386 Lambda K H 0.319 0.136 0.394 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: 652 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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: 50 (23.9 bits)
Align candidate 17978 b3939 (cystathionine gamma-synthase (NCBI))
to HMM TIGR02080 (metB: O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48))
# 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/TIGR02080.hmm # target sequence database: /tmp/gapView.21361.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02080 [M=382] Accession: TIGR02080 Description: O_succ_thio_ly: O-succinylhomoserine (thiol)-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-216 702.9 0.0 4.7e-216 702.7 0.0 1.0 1 lcl|FitnessBrowser__Keio:17978 b3939 cystathionine gamma-syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17978 b3939 cystathionine gamma-synthase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 702.7 0.0 4.7e-216 4.7e-216 2 381 .. 3 382 .. 2 383 .. 1.00 Alignments for each domain: == domain 1 score: 702.7 bits; conditional E-value: 4.7e-216 TIGR02080 2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvtssGmsaie 80 rk+atiavrsGl++d+qyg+vvpPi+ls+ty+f+gfnepra+dysr+gnPtrd++++alaele+Ga+av+t++Gmsai+ lcl|FitnessBrowser__Keio:17978 3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIH 81 89***************************************************************************** PP TIGR02080 81 llviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlietPsnPllrvvdiaklc 159 l+++++lkp+dllvaPhdcyGG+yrl+++lak+g+++v++vdq de+al++alaekpklvl+e+PsnPllrvvdiak+c lcl|FitnessBrowser__Keio:17978 82 LVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKIC 160 ******************************************************************************* PP TIGR02080 160 klakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakdkqlaeelawwanalGvtgaafdsy 238 +la+++gav+vvdntflsP+lq+PlalGadlvlhs+tkylnGhsdv+aG+viakd+++++elawwan++Gvtg+afdsy lcl|FitnessBrowser__Keio:17978 161 HLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSY 239 ******************************************************************************* PP TIGR02080 239 lllrGlrtlaarvreqernakkiveylqkqplvkkvyypglpdhagheiaakqqkGfGallsfelkGgeeevkkflkkl 317 lllrGlrtl+ r++ ++rna++iv+ylq+qplvkk+y+p+lp+++gheiaa+qqkGfGa+lsfel+G+e+++++fl+ l lcl|FitnessBrowser__Keio:17978 240 LLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGL 318 ******************************************************************************* PP TIGR02080 318 klftlaeslGGvesliahpatmthaamekeareeaGikdellrlsvGledaddliadleqalaa 381 +lftlaeslGGvesli+h+atmtha+m++ear++aGi+++llr+s+G+ed++dliadle++++a lcl|FitnessBrowser__Keio:17978 319 SLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRA 382 **************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (382 nodes) Target sequences: 1 (386 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: 00:00:00.01 # Mc/sec: 9.33 // [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