Align Cysteine synthase; CSase; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase; EC 2.5.1.47 (characterized)
to candidate Synpcc7942_B2664 Synpcc7942_B2664 cysteine synthase
Query= SwissProt::Q59966 (329 letters) >FitnessBrowser__SynE:Synpcc7942_B2664 Length = 329 Score = 639 bits (1648), Expect = 0.0 Identities = 329/329 (100%), Positives = 329/329 (100%) Query: 1 MSTSGTFFADNSQTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAE 60 MSTSGTFFADNSQTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAE Sbjct: 1 MSTSGTFFADNSQTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAE 60 Query: 61 QRGLLGPGKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLT 120 QRGLLGPGKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLT Sbjct: 61 QRGLLGPGKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLT 120 Query: 121 EGVKGMTGAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVS 180 EGVKGMTGAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVS Sbjct: 121 EGVKGMTGAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVS 180 Query: 181 GVGTGGTITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFI 240 GVGTGGTITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFI Sbjct: 181 GVGTGGTITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFI 240 Query: 241 PENLDLSLVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTI 300 PENLDLSLVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTI Sbjct: 241 PENLDLSLVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTI 300 Query: 301 VVVLPDSGERYLSTALFDGIFNEQGLAVV 329 VVVLPDSGERYLSTALFDGIFNEQGLAVV Sbjct: 301 VVVLPDSGERYLSTALFDGIFNEQGLAVV 329 Lambda K H 0.316 0.134 0.378 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: 551 Number of extensions: 17 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: 329 Length of database: 329 Length adjustment: 28 Effective length of query: 301 Effective length of database: 301 Effective search space: 90601 Effective search space used: 90601 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: 49 (23.5 bits)
Align candidate Synpcc7942_B2664 Synpcc7942_B2664 (cysteine synthase)
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))
# 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/TIGR01139.hmm # target sequence database: /tmp/gapView.22035.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01139 [M=298] Accession: TIGR01139 Description: cysK: cysteine synthase A 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-143 461.2 0.1 8.3e-143 461.0 0.1 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_B2664 Synpcc7942_B2664 cysteine syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_B2664 Synpcc7942_B2664 cysteine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.0 0.1 8.3e-143 8.3e-143 2 298 .] 12 317 .. 11 317 .. 0.99 Alignments for each domain: == domain 1 score: 461.0 bits; conditional E-value: 8.3e-143 TIGR01139 2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGnt 68 s++iG+tPlvrLn ++++a a vl+k+e +nP++svk+ri++ami+dae++gll +gk+++e+tsGnt lcl|FitnessBrowser__SynE:Synpcc7942_B2664 12 SQTIGKTPLVRLNrIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAEQRGLLGPGKELIEPTSGNT 79 789**********9999*************************************************** PP TIGR01139 69 GialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylll 136 Giala+vaaarg l+ltmpetmslerrkll ayGa+lvLt+g +gm+ga+++ae++++++p++y+ll lcl|FitnessBrowser__SynE:Synpcc7942_B2664 80 GIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGVKGMTGAVRRAEDIAASDPDRYVLL 147 ******************************************************************** PP TIGR01139 137 kqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespv 203 +qf npanp+ih++tt+pei++d+ g++d++v+gvGtGGtitGv++++k++++ i +vaveP++spv lcl|FitnessBrowser__SynE:Synpcc7942_B2664 148 QQFRNPANPAIHEQTTGPEIWEDTGGAIDILVSGVGTGGTITGVSRYIKQTQGkPILSVAVEPEASPV 215 **************************************************99978************* PP TIGR01139 204 lsgg......kpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaav 265 +s++ kpgphkiqGigagfiP++Ld +++d+v +vs+eeai++arrla+eeG+++Gis Gaav lcl|FitnessBrowser__SynE:Synpcc7942_B2664 216 ISQQrsglplKPGPHKIQGIGAGFIPENLDLSLVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAV 283 ***999************************************************************** PP TIGR01139 266 aaalkvakkle.kdkkivvilpdtgerYlstaLf 298 aaa+++a++ e ++k+ivv+lpd+gerYlstaLf lcl|FitnessBrowser__SynE:Synpcc7942_B2664 284 AAAVRLAQQSEhAGKTIVVVLPDSGERYLSTALF 317 **********99*********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (329 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: 11.80 // [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