Align S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF1601 Psest_1638 cysteine synthase B
Query= BRENDA::P29848 (303 letters) >FitnessBrowser__psRCH2:GFF1601 Length = 300 Score = 408 bits (1048), Expect = e-119 Identities = 204/290 (70%), Positives = 235/290 (81%) Query: 3 TLEQTIGNTPLVKLQRLGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGD 62 T+ IGNTPLV+LQR+ + I VKLEGNNPAGSVKDR ALSMI AE RG+I+PGD Sbjct: 7 TIADCIGNTPLVRLQRMPGKTSNTILVKLEGNNPAGSVKDRPALSMINRAELRGDIQPGD 66 Query: 63 VLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGA 122 LIEATSGNTGIALAM AA+KGYRM L+MPDN + ER+AAM AYGAELILV+KE+GMEGA Sbjct: 67 TLIEATSGNTGIALAMAAAIKGYRMILIMPDNSTAERKAAMTAYGAELILVSKEEGMEGA 126 Query: 123 RDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTITGV 182 RDLAL M G GK+LDQF N DNP AHY +TGPE+WRQT G ITHF+SSMGTTGTI GV Sbjct: 127 RDLALKMQAEGRGKVLDQFANGDNPEAHYNSTGPELWRQTHGSITHFISSMGTTGTIMGV 186 Query: 183 SRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENTMR 242 SR+L+EQ V IVGLQP EG++IPGIRRWP EY+P I+ A VD V+D+ Q +AE MR Sbjct: 187 SRYLKEQNPAVQIVGLQPMEGAAIPGIRRWPQEYLPKIYQAERVDRVVDMSQAEAEQVMR 246 Query: 243 ELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVF 292 LA EGIFCGVSSGGAVA ALR+++ A++VAIICDRGDRYLSTGV+ Sbjct: 247 RLAREEGIFCGVSSGGAVAAALRLSQEVENAVIVAIICDRGDRYLSTGVY 296 Lambda K H 0.316 0.134 0.386 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: 372 Number of extensions: 9 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: 303 Length of database: 300 Length adjustment: 27 Effective length of query: 276 Effective length of database: 273 Effective search space: 75348 Effective search space used: 75348 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: 48 (23.1 bits)
Align candidate GFF1601 Psest_1638 (cysteine synthase B)
to HMM TIGR01138 (cysM: cysteine synthase B (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/TIGR01138.hmm # target sequence database: /tmp/gapView.13404.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01138 [M=290] Accession: TIGR01138 Description: cysM: cysteine synthase B 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-166 539.0 0.4 1.8e-166 538.9 0.4 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1601 Psest_1638 cysteine synthase B Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1601 Psest_1638 cysteine synthase B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 538.9 0.4 1.8e-166 1.8e-166 1 290 [] 7 296 .. 7 296 .. 1.00 Alignments for each domain: == domain 1 score: 538.9 bits; conditional E-value: 1.8e-166 TIGR01138 1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGiala 75 ti++++Gntplvrl+r+++++++++lvklegnnpaGsvkdrpalsmi +ae+rG+i++Gd+lieatsGntGiala lcl|FitnessBrowser__psRCH2:GFF1601 7 TIADCIGNTPLVRLQRMPGKTSNTILVKLEGNNPAGSVKDRPALSMINRAELRGDIQPGDTLIEATSGNTGIALA 81 89************************************************************************* PP TIGR01138 76 mvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahyt 150 m+aa+kGy+++l+mpdn+++erkaa++ayGaelilv+keeGmeGardla +++ +g++k+ldqf+n+dnp+ahy+ lcl|FitnessBrowser__psRCH2:GFF1601 82 MAAAIKGYRMILIMPDNSTAERKAAMTAYGAELILVSKEEGMEGARDLALKMQAEGRGKVLDQFANGDNPEAHYN 156 *************************************************************************** PP TIGR01138 151 stGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslvd 225 stG+e+w+qt G+ithf+ss+GttGtimGvsr+lkeqnpavqivGlqp+eg ai+G+rr+++eylp+i++a +vd lcl|FitnessBrowser__psRCH2:GFF1601 157 STGPELWRQTHGSITHFISSMGTTGTIMGVSRYLKEQNPAVQIVGLQPMEGAAIPGIRRWPQEYLPKIYQAERVD 231 *************************************************************************** PP TIGR01138 226 rvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290 rvvd+ q +ae+++r+la++egif+GvssGgavaaalrl++e+e+av+vaiicdrGdrylstgv+ lcl|FitnessBrowser__psRCH2:GFF1601 232 RVVDMSQAEAEQVMRRLAREEGIFCGVSSGGAVAAALRLSQEVENAVIVAIICDRGDRYLSTGVY 296 ****************************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (300 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: 6.11 // [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