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 Dsui_1954 Dsui_1954 cysteine synthase B
Query= BRENDA::P29848 (303 letters) >FitnessBrowser__PS:Dsui_1954 Length = 299 Score = 369 bits (946), Expect = e-107 Identities = 187/294 (63%), Positives = 225/294 (76%), Gaps = 4/294 (1%) Query: 3 TLEQTIGNTPLVKLQRLGPD----NGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEI 58 TLE +GNTPLV+L+RL + G+ I KLEGNNPAGSVKDR ALSMI AE+RGEI Sbjct: 4 TLEDFVGNTPLVQLKRLPGEAIAQRGNVILAKLEGNNPAGSVKDRPALSMISHAEQRGEI 63 Query: 59 KPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQG 118 +PGD LIEATSGNTGIALAM AA++GYRM L+MP+N S ERR MRAYGAELIL ++ G Sbjct: 64 RPGDTLIEATSGNTGIALAMAAAMRGYRMILVMPENQSLERRQTMRAYGAELILTPRDGG 123 Query: 119 MEGARDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGT 178 ME ARD+A M + G+G +LDQF NPDNP AH+ TGPEIWR T G++THFVSSMGTTGT Sbjct: 124 MELARDVAEKMCDEGKGIILDQFANPDNPLAHFEGTGPEIWRDTKGQVTHFVSSMGTTGT 183 Query: 179 ITGVSRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAE 238 I G S+FL+++ + IVG QPEEGS IPGIR+WP Y+P I+ S VD + + Q +AE Sbjct: 184 IIGTSQFLKKKNPRIQIVGCQPEEGSQIPGIRKWPEAYLPKIYERSRVDRLEYVSQAEAE 243 Query: 239 NTMRELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVF 292 + R LA EG+F G+SSGGA+A ALR+AR A +V I+CDRGDRYLSTGVF Sbjct: 244 DMTRRLAREEGLFAGISSGGALAVALRLARELENATIVTIVCDRGDRYLSTGVF 297 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: 356 Number of extensions: 14 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: 303 Length of database: 299 Length adjustment: 27 Effective length of query: 276 Effective length of database: 272 Effective search space: 75072 Effective search space used: 75072 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 Dsui_1954 Dsui_1954 (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.21378.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-143 463.1 0.0 2.3e-143 463.0 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_1954 Dsui_1954 cysteine synthase B Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1954 Dsui_1954 cysteine synthase B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.0 0.0 2.3e-143 2.3e-143 1 290 [] 4 297 .. 4 297 .. 0.99 Alignments for each domain: == domain 1 score: 463.0 bits; conditional E-value: 2.3e-143 TIGR01138 1 tilklvGntplvrlkrllpe....edsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGia 73 t+++ vGntplv+lkrl++e ++ +l+klegnnpaGsvkdrpalsmi +ae+rGei++Gd+lieatsGntGia lcl|FitnessBrowser__PS:Dsui_1954 4 TLEDFVGNTPLVQLKRLPGEaiaqRGNVILAKLEGNNPAGSVKDRPALSMISHAEQRGEIRPGDTLIEATSGNTGIA 80 899*****************99988999************************************************* PP TIGR01138 74 lamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahyt 150 lam+aa++Gy+++l+mp+n s er++ ++ayGaelil+ ++ Gme ard+a+++ ++g++ +ldqf+npdnp ah+ lcl|FitnessBrowser__PS:Dsui_1954 81 LAMAAAMRGYRMILVMPENQSLERRQTMRAYGAELILTPRDGGMELARDVAEKMCDEGKGIILDQFANPDNPLAHFE 157 ***************************************************************************** PP TIGR01138 151 stGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslvdrv 227 tG+eiw+ tkG++thfvss+GttGti+G+s+flk++np +qivG qp+egs+i+G+r++++ ylp+i++ s+vdr lcl|FitnessBrowser__PS:Dsui_1954 158 GTGPEIWRDTKGQVTHFVSSMGTTGTIIGTSQFLKKKNPRIQIVGCQPEEGSQIPGIRKWPEAYLPKIYERSRVDRL 234 ***************************************************************************** PP TIGR01138 228 vdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290 +v q +aed+ r+la++eg+f G+ssGga+a alrlarele+a +v+i+cdrGdrylstgvf lcl|FitnessBrowser__PS:Dsui_1954 235 EYVSQAEAEDMTRRLAREEGLFAGISSGGALAVALRLARELENATIVTIVCDRGDRYLSTGVF 297 **************************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (299 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: 8.10 // [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