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 Pf1N1B4_3506 Cysteine synthase B (EC 2.5.1.47)
Query= BRENDA::P29848 (303 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 Length = 300 Score = 402 bits (1034), Expect = e-117 Identities = 200/290 (68%), Positives = 233/290 (80%) Query: 3 TLEQTIGNTPLVKLQRLGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGD 62 T+ +GNTPLV+LQRL + + +KLEGNNPAGSVKDR ALSMI AE RG+I GD Sbjct: 7 TIADCVGNTPLVRLQRLPGATSNTLLLKLEGNNPAGSVKDRPALSMITRAELRGQIHAGD 66 Query: 63 VLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGA 122 LIEATSGNTGIALAM AA+KGY+M L+MPDN S ER+AAM AYGAELILV++E+GMEGA Sbjct: 67 TLIEATSGNTGIALAMAAAIKGYKMILIMPDNSSAERKAAMTAYGAELILVSQEEGMEGA 126 Query: 123 RDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTITGV 182 RDLA M G GK+LDQF N DNP AHYTTTGPEIWRQT G ITHFVSSMGTTGTI GV Sbjct: 127 RDLAQRMEAEGRGKVLDQFANGDNPEAHYTTTGPEIWRQTEGTITHFVSSMGTTGTIMGV 186 Query: 183 SRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENTMR 242 SR+L+EQ V I+GLQP EGS+IPGIRRWP EY+P I+ A VD ++D+ Q++AE+ R Sbjct: 187 SRYLKEQNDNVQIIGLQPMEGSAIPGIRRWPQEYLPKIYQAERVDRIVDMAQSEAEDVTR 246 Query: 243 ELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVF 292 LA EGIFCGVSSGGAVA LR+++ A++VAIICDRGDRYLSTG+F Sbjct: 247 RLAREEGIFCGVSSGGAVAAMLRLSKEVENAVIVAIICDRGDRYLSTGIF 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: 367 Number of extensions: 11 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 Pf1N1B4_3506 (Cysteine synthase B (EC 2.5.1.47))
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.5112.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-165 535.0 0.5 3e-165 534.8 0.5 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 Cysteine synthase B (EC 2.5.1.47 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 Cysteine synthase B (EC 2.5.1.47) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.8 0.5 3e-165 3e-165 1 290 [] 7 296 .. 7 296 .. 1.00 Alignments for each domain: == domain 1 score: 534.8 bits; conditional E-value: 3e-165 TIGR01138 1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlie 64 ti+++vGntplvrl+rl++ +++++l+klegnnpaGsvkdrpalsmi++ae+rG+i+ Gd+lie lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 7 TIADCVGNTPLVRLQRLPGATSNTLLLKLEGNNPAGSVKDRPALSMITRAELRGQIHAGDTLIE 70 89************************************************************** PP TIGR01138 65 atsGntGialamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelv 128 atsGntGialam+aa+kGyk++l+mpdn+s+erkaa++ayGaelilv++eeGmeGardla+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 71 ATSGNTGIALAMAAAIKGYKMILIMPDNSSAERKAAMTAYGAELILVSQEEGMEGARDLAQRME 134 **************************************************************** PP TIGR01138 129 rkgeeklldqfnnpdnpkahytstGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavq 192 +g++k+ldqf+n+dnp+ahyt+tG+eiw+qt+G ithfvss+GttGtimGvsr+lkeqn++vq lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 135 AEGRGKVLDQFANGDNPEAHYTTTGPEIWRQTEGTITHFVSSMGTTGTIMGVSRYLKEQNDNVQ 198 **************************************************************** PP TIGR01138 193 ivGlqpaegsaieGlrrieseylpgifdaslvdrvvdveqedaediarelakkegifvGvssGg 256 i+Glqp+egsai+G+rr+++eylp+i++a +vdr+vd+ q++aed+ r+la++egif+GvssGg lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 199 IIGLQPMEGSAIPGIRRWPQEYLPKIYQAERVDRIVDMAQSEAEDVTRRLAREEGIFCGVSSGG 262 **************************************************************** PP TIGR01138 257 avaaalrlarelekavvvaiicdrGdrylstgvf 290 avaa+lrl++e+e+av+vaiicdrGdrylstg+f lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3506 263 AVAAMLRLSKEVENAVIVAIICDRGDRYLSTGIF 296 ********************************98 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.71 // [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