Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_012589377.1 MSIL_RS01685 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::P00935 (386 letters) >NCBI__GCF_000021745.1:WP_012589377.1 Length = 385 Score = 408 bits (1049), Expect = e-118 Identities = 209/384 (54%), Positives = 267/384 (69%), Gaps = 3/384 (0%) Query: 1 MTRKQA--TIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQ 58 MT ++A TIA +G+ D YG PPI+LSST+ F GF P H+Y+R NPTRD++ Sbjct: 1 MTHEKALQTIAASNGVAADSAYGAAAPPIYLSSTFAFKGFERPGGHEYTRTSNPTRDLLA 60 Query: 59 RALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYR 118 LA+LEGGAGAV ++GM+AI+L+ ++ DL++APHDCY G RL + A +G ++ Sbjct: 61 DTLAKLEGGAGAVTLSSGMAAINLLLDP-MERDDLVIAPHDCYSGVQRLLSAHAAKGHFK 119 Query: 119 VLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLS 178 V FVDQ D +A+ AL PKL+++E+PSNPL+RVVDI C A++VGA VDNTFLS Sbjct: 120 VEFVDQSDAEAVATALGRNPKLLMIETPSNPLMRVVDIRAFCEAAKKVGAKVAVDNTFLS 179 Query: 179 PALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDS 238 PALQ P+ LGAD V+HS TK+LNGHSDVV G VI E+ WAN GVTG FDS Sbjct: 180 PALQRPIPLGADFVVHSMTKFLNGHSDVVGGAVICASESDAEEMRGWANITGVTGSPFDS 239 Query: 239 YLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGA 298 YL LRGLRTL PR+E QR A+ I +LQ P V+ +++P L + H +A QQ GFGA Sbjct: 240 YLTLRGLRTLFPRLERQQRTAETIALFLQQHPSVEAVHYPGLVSHPSHALAKAQQAGFGA 299 Query: 299 MLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISET 358 MLSFE+ G +RR + + +FTLAESLGGVESLI+H ATMTHA MAPEARAAAGI + Sbjct: 300 MLSFEVAGGIAAVRRLVESVRIFTLAESLGGVESLIAHPATMTHASMAPEARAAAGIKDN 359 Query: 359 LLRISTGIEDGEDLIADLENGFRA 382 LLR+S G+E DL++DL +A Sbjct: 360 LLRLSVGLEHEGDLVSDLAQALKA 383 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: 415 Number of extensions: 10 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: 385 Length adjustment: 30 Effective length of query: 356 Effective length of database: 355 Effective search space: 126380 Effective search space used: 126380 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 WP_012589377.1 MSIL_RS01685 (O-succinylhomoserine (thiol)-lyase)
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.19801.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-176 571.0 0.0 5.9e-176 570.7 0.0 1.0 1 lcl|NCBI__GCF_000021745.1:WP_012589377.1 MSIL_RS01685 O-succinylhomoserin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021745.1:WP_012589377.1 MSIL_RS01685 O-succinylhomoserine (thiol)-lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 570.7 0.0 5.9e-176 5.9e-176 4 381 .. 7 383 .. 4 384 .. 0.99 Alignments for each domain: == domain 1 score: 570.7 bits; conditional E-value: 5.9e-176 TIGR02080 4 katiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvt 72 +tia+ +G++ d++yga pPiyls+t++f+gf++p ++y+r+ nPtrdll+++la+le+Ga+av lcl|NCBI__GCF_000021745.1:WP_012589377.1 7 LQTIAASNGVAADSAYGAAAPPIYLSSTFAFKGFERPGGHEYTRTSNPTRDLLADTLAKLEGGAGAVTL 75 68******************************************************************* PP TIGR02080 73 ssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvl 141 ssGm+ai+ll+ +++ddl++aPhdcy G rll+a a kg++kv++vdqsd+ea++ al ++pkl++ lcl|NCBI__GCF_000021745.1:WP_012589377.1 76 SSGMAAINLLL-DPMERDDLVIAPHDCYSGVQRLLSAHAAKGHFKVEFVDQSDAEAVATALGRNPKLLM 143 **********9.999****************************************************** PP TIGR02080 142 ietPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGav 210 ietPsnPl+rvvdi+++c++ak++ga v+vdntflsP+lq+P+ lGad+v+hs tk+lnGhsdv++Gav lcl|NCBI__GCF_000021745.1:WP_012589377.1 144 IETPSNPLMRVVDIRAFCEAAKKVGAKVAVDNTFLSPALQRPIPLGADFVVHSMTKFLNGHSDVVGGAV 212 ********************************************************************* PP TIGR02080 211 iakdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypgl 279 i++ ++ aee++ wan +Gvtg++fdsyl+lrGlrtl+ r+++q+r+a++i+ +lq++p v+ v+ypgl lcl|NCBI__GCF_000021745.1:WP_012589377.1 213 ICASESDAEEMRGWANITGVTGSPFDSYLTLRGLRTLFPRLERQQRTAETIALFLQQHPSVEAVHYPGL 281 ********************************************************************* PP TIGR02080 280 pdhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesliahpatmthaamekea 348 +h+ h++a+ qq GfGa+lsfe++Gg ++v+++++++++ftlaeslGGvesliahpatmtha+m++ea lcl|NCBI__GCF_000021745.1:WP_012589377.1 282 VSHPSHALAKAQQAGFGAMLSFEVAGGIAAVRRLVESVRIFTLAESLGGVESLIAHPATMTHASMAPEA 350 ********************************************************************* PP TIGR02080 349 reeaGikdellrlsvGledaddliadleqalaa 381 r++aGikd+llrlsvGle+ dl++dl qal+a lcl|NCBI__GCF_000021745.1:WP_012589377.1 351 RAAAGIKDNLLRLSVGLEHEGDLVSDLAQALKA 383 ******************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (382 nodes) Target sequences: 1 (385 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: 12.30 // [ok]
This GapMind analysis is from Apr 10 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