Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 6939073 Sama_3171 cystathionine gamma-synthase (RefSeq)
Query= SwissProt::P00935 (386 letters) >FitnessBrowser__SB2B:6939073 Length = 386 Score = 461 bits (1186), Expect = e-134 Identities = 234/380 (61%), Positives = 287/380 (75%), Gaps = 1/380 (0%) Query: 3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALA 62 RK ATIAVR G+ D Q+G VVPPI+LS+ Y+F G PR DYSR GNPTR ++ ALA Sbjct: 4 RKAATIAVRQGIESDTQHGAVVPPIYLSTNYSFDGHKNPRKFDYSRSGNPTRCILGEALA 63 Query: 63 ELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFV 122 ELE GA ++T TGM+AI LVT++ L P DLLV PHDCYGGSYRLF +LAK+G +++ V Sbjct: 64 ELEQGATGIITCTGMAAITLVTSL-LGPDDLLVVPHDCYGGSYRLFTNLAKKGAFKLAVV 122 Query: 123 DQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQ 182 DQ D+ AL A +A+KP++V +E+PSNPLLRVVDI I + EVGA+ VVDNTFLSP LQ Sbjct: 123 DQTDDAALAAVIAQKPRMVWLETPSNPLLRVVDIQAISDASHEVGALVVVDNTFLSPILQ 182 Query: 183 NPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLL 242 PL LGAD+V+HS TKY+NGHSDVV G VIA+D ++ L WW+N +G+TG AFDSYL L Sbjct: 183 QPLLLGADIVIHSTTKYINGHSDVVGGAVIARDAELGETLHWWSNTLGLTGSAFDSYLTL 242 Query: 243 RGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSF 302 RG+RTL R+ Q NAQ IV L+ P V K+Y+P L ++ GH+IAARQQKGFGAMLSF Sbjct: 243 RGIRTLAVRVREHQSNAQRIVDVLKNSPQVSKVYYPGLADHPGHDIAARQQKGFGAMLSF 302 Query: 303 ELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRI 362 EL G E+ L FL L F++AESLGGVESL++ ATMTH M PEARA AGI +TLLR+ Sbjct: 303 ELVGGEKELVAFLDALQHFSVAESLGGVESLVAVPATMTHRAMVPEARAEAGIKDTLLRL 362 Query: 363 STGIEDGEDLIADLENGFRA 382 S GIED EDL+AD++ G A Sbjct: 363 SVGIEDAEDLVADIQAGLAA 382 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: 466 Number of extensions: 14 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: 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 6939073 Sama_3171 (cystathionine gamma-synthase (RefSeq))
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.23534.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-205 665.9 0.1 8.3e-205 665.7 0.1 1.0 1 lcl|FitnessBrowser__SB2B:6939073 Sama_3171 cystathionine gamma-sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6939073 Sama_3171 cystathionine gamma-synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 665.7 0.1 8.3e-205 8.3e-205 2 382 .] 4 383 .. 3 383 .. 0.99 Alignments for each domain: == domain 1 score: 665.7 bits; conditional E-value: 8.3e-205 TIGR02080 2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvtssGmsa 78 rk+atiavr+G+esd+q+gavvpPiylst+y+f+g+++pr++dysrsgnPtr +l +alaele+Ga++++t++Gm+a lcl|FitnessBrowser__SB2B:6939073 4 RKAATIAVRQGIESDTQHGAVVPPIYLSTNYSFDGHKNPRKFDYSRSGNPTRCILGEALAELEQGATGIITCTGMAA 80 799************************************************************************** PP TIGR02080 79 iellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlietPsnPllrvvdi 155 i+l++ +ll+pddllv+PhdcyGG+yrl+++lakkg +k+ +vdq+d +al++++a+kp++v++etPsnPllrvvdi lcl|FitnessBrowser__SB2B:6939073 81 ITLVT-SLLGPDDLLVVPHDCYGGSYRLFTNLAKKGAFKLAVVDQTDDAALAAVIAQKPRMVWLETPSNPLLRVVDI 156 ***99.*********************************************************************** PP TIGR02080 156 aklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakdkqlaeelawwanalGvtg 232 ++++++++++ga+vvvdntflsPilq+Pl lGad+v+hs+tky+nGhsdv++Gavia+d +l e+l+ww+n+lG+tg lcl|FitnessBrowser__SB2B:6939073 157 QAISDASHEVGALVVVDNTFLSPILQQPLLLGADIVIHSTTKYINGHSDVVGGAVIARDAELGETLHWWSNTLGLTG 233 ***************************************************************************** PP TIGR02080 233 aafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypglpdhagheiaakqqkGfGallsfelkGgeee 309 +afdsyl+lrG+rtla+rvre++ na++iv+ l+++p+v+kvyypgl+dh+gh+iaa+qqkGfGa+lsfel Gge+e lcl|FitnessBrowser__SB2B:6939073 234 SAFDSYLTLRGIRTLAVRVREHQSNAQRIVDVLKNSPQVSKVYYPGLADHPGHDIAARQQKGFGAMLSFELVGGEKE 310 ***************************************************************************** PP TIGR02080 310 vkkflkklklftlaeslGGvesliahpatmthaamekeareeaGikdellrlsvGledaddliadleqalaav 382 + +fl++l+ f++aeslGGvesl+a+patmth+am +ear+eaGikd+llrlsvG+eda+dl+ad++++laav lcl|FitnessBrowser__SB2B:6939073 311 LVAFLDALQHFSVAESLGGVESLVAVPATMTHRAMVPEARAEAGIKDTLLRLSVGIEDAEDLVADIQAGLAAV 383 **********************************************************************985 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.05 // [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