Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF1476 PS417_07505 cysteine synthase
Query= BRENDA::P0ABK5 (323 letters) >FitnessBrowser__WCS417:GFF1476 Length = 324 Score = 442 bits (1138), Expect = e-129 Identities = 229/324 (70%), Positives = 264/324 (81%), Gaps = 3/324 (0%) Query: 1 MSKIFEDNSLTIGHTPLVRLNRIG--NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGV 58 MS+IF DN+ +IG+TPLV++NRI ILAK+E RNP +SVKCRIGANMIWDAE G Sbjct: 1 MSRIFADNAHSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGK 60 Query: 59 LKPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAK 118 LKPG+ +VEPTSGNTGI LA+VAAARGYKL LTMP +MSIERRK+LKALGA LVLTE AK Sbjct: 61 LKPGMTIVEPTSGNTGIGLAFVAAARGYKLLLTMPASMSIERRKVLKALGAELVLTEPAK 120 Query: 119 GMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGT 178 GMKGAI+KA EIVAS+P Y + QF NPANP IHEKTTGPEIW DTDG VDV +AGVGT Sbjct: 121 GMKGAIEKAGEIVASDPATYFMPAQFENPANPAIHEKTTGPEIWNDTDGAVDVLVAGVGT 180 Query: 179 GGTLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPAN 238 GGT+TGVSRYIK GK ++SVAVEP SPVI QALAGEEIKP PHKIQGIGAGF+P N Sbjct: 181 GGTITGVSRYIKNIAGK-PILSVAVEPIVSPVITQALAGEEIKPSPHKIQGIGAGFVPKN 239 Query: 239 LDLKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVI 298 LDL +VD+V +T++E+ + A RLM+EEGIL GIS GAA+A A++L E K IVVI Sbjct: 240 LDLSMVDRVELVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEMQGKTIVVI 299 Query: 299 LPSSGERYLSTALFADLFTEKELQ 322 LP SGERYLS+ LF+DLFTE+E Q Sbjct: 300 LPDSGERYLSSMLFSDLFTEQENQ 323 Lambda K H 0.313 0.133 0.368 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: 405 Number of extensions: 18 Number of successful extensions: 3 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: 323 Length of database: 324 Length adjustment: 28 Effective length of query: 295 Effective length of database: 296 Effective search space: 87320 Effective search space used: 87320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate GFF1476 PS417_07505 (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.1164436.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-138 445.4 0.8 5.4e-138 445.2 0.8 1.0 1 FitnessBrowser__WCS417:GFF1476 Domain annotation for each sequence (and alignments): >> FitnessBrowser__WCS417:GFF1476 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.2 0.8 5.4e-138 5.4e-138 3 298 .] 10 313 .. 8 313 .. 0.99 Alignments for each domain: == domain 1 score: 445.2 bits; conditional E-value: 5.4e-138 TIGR01139 3 eliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaargy 81 + iGntPlv++n++++ + +l+k+e +nP++svk+ri+++mi+dae +g+lk+g tive+tsGntGi+la+vaaargy FitnessBrowser__WCS417:GFF1476 10 HSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGKLKPGMTIVEPTSGNTGIGLAFVAAARGY 88 78***************************************************************************** PP TIGR01139 82 kliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttapeilkdl 160 kl+ltmp++ms+errk+lka+GaelvLt++a+gmkgaieka e+v+++p +y+++ qfenpanp+ih+ktt+pei++d+ FitnessBrowser__WCS417:GFF1476 89 KLLLTMPASMSIERRKVLKALGAELVLTEPAKGMKGAIEKAGEIVASDPATYFMPAQFENPANPAIHEKTTGPEIWNDT 167 ******************************************************************************* PP TIGR01139 161 dgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigagfiPkvLdkevid 232 dg++d++vagvGtGGtitGv++++k+ + i +vaveP spv++++ kp phkiqGigagf+Pk+Ld +++d FitnessBrowser__WCS417:GFF1476 168 DGAVDVLVAGVGTGGTITGVSRYIKNIAGkPILSVAVEPIVSPVITQAlageeiKPSPHKIQGIGAGFVPKNLDLSMVD 246 **************************99868****************9999999************************* PP TIGR01139 233 evikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298 +v v+d+e+ ++a rl++eeGil Gis Gaa+a a+++a+k+e ++k+ivvilpd+gerYls Lf FitnessBrowser__WCS417:GFF1476 247 RVELVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEmQGKTIVVILPDSGERYLSSMLF 313 ********************************************9*******************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (324 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 19.47 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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