Align Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 (characterized)
to candidate WP_086510266.1 BZY95_RS12545 cysteine synthase CysM
Query= SwissProt::P16703 (303 letters) >NCBI__GCF_002151265.1:WP_086510266.1 Length = 298 Score = 395 bits (1015), Expect = e-115 Identities = 199/293 (67%), Positives = 235/293 (80%) Query: 3 TLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGD 62 T+E +G+TPLV+L+R+ + + KLEGNNPAGSVKDR ALSM+ +AE RG+I PGD Sbjct: 5 TIEDVVGHTPLVRLKRITAGRNNTLLAKLEGNNPAGSVKDRPALSMLEQAEARGDITPGD 64 Query: 63 VLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGA 122 LIEATSGNTGIALAM AA+KGYRM L+MPD+ S ER+ AM AYGA LI V+KE GME A Sbjct: 65 TLIEATSGNTGIALAMAAAIKGYRMVLIMPDSASSERKQAMAAYGARLITVSKEGGMEEA 124 Query: 123 RDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGV 182 RDLA M +RGEGK L+QF NPDNP AHY TGPE+W+QTGG ITHFVSSMGTTGTI GV Sbjct: 125 RDLAEAMVSRGEGKPLNQFANPDNPLAHYRGTGPELWEQTGGTITHFVSSMGTTGTIMGV 184 Query: 183 SRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMR 242 SR+++E++ V IVGLQPE+G+SI GIRRWP EYLP IF+A+ VD VLDI Q +AE MR Sbjct: 185 SRYLKERNPEVQIVGLQPEDGASIAGIRRWPKEYLPSIFDATRVDRVLDIGQHEAEEHMR 244 Query: 243 ELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEE 295 LA EGI GVSSGGA+AGALRVA+ +AV+V I+CDRGDRYLSTG+F E Sbjct: 245 RLAREEGILAGVSSGGALAGALRVAEEVENAVIVFIVCDRGDRYLSTGLFAPE 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: 353 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: 298 Length adjustment: 27 Effective length of query: 276 Effective length of database: 271 Effective search space: 74796 Effective search space used: 74796 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 WP_086510266.1 BZY95_RS12545 (cysteine synthase CysM)
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.22501.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-149 482.1 0.1 3.9e-149 481.9 0.1 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510266.1 BZY95_RS12545 cysteine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510266.1 BZY95_RS12545 cysteine synthase CysM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 481.9 0.1 3.9e-149 3.9e-149 1 290 [] 5 294 .. 5 294 .. 1.00 Alignments for each domain: == domain 1 score: 481.9 bits; conditional E-value: 3.9e-149 TIGR01138 1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGn 69 ti+++vG tplvrlkr+++ ++++l+klegnnpaGsvkdrpalsm+ +ae rG+i +Gd+lieatsGn lcl|NCBI__GCF_002151265.1:WP_086510266.1 5 TIEDVVGHTPLVRLKRITAGRNNTLLAKLEGNNPAGSVKDRPALSMLEQAEARGDITPGDTLIEATSGN 73 89******************************************************************* PP TIGR01138 70 tGialamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldq 138 tGialam+aa+kGy++ l+mpd s erk+a+ ayGa+li v+ke Gme ardla+ +v +ge+k l+q lcl|NCBI__GCF_002151265.1:WP_086510266.1 74 TGIALAMAAAIKGYRMVLIMPDSASSERKQAMAAYGARLITVSKEGGMEEARDLAEAMVSRGEGKPLNQ 142 ********************************************************************* PP TIGR01138 139 fnnpdnpkahytstGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGl 207 f+npdnp ahy tG+e+w+qt+G ithfvss+GttGtimGvsr+lke+np+vqivGlqp++g +i G+ lcl|NCBI__GCF_002151265.1:WP_086510266.1 143 FANPDNPLAHYRGTGPELWEQTGGTITHFVSSMGTTGTIMGVSRYLKERNPEVQIVGLQPEDGASIAGI 211 ********************************************************************* PP TIGR01138 208 rrieseylpgifdaslvdrvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvai 276 rr+++eylp ifda++vdrv+d+ q++ae+ +r+la++egi+ GvssGga+a+alr+a e+e+av+v i lcl|NCBI__GCF_002151265.1:WP_086510266.1 212 RRWPKEYLPSIFDATRVDRVLDIGQHEAEEHMRRLAREEGILAGVSSGGALAGALRVAEEVENAVIVFI 280 ********************************************************************* PP TIGR01138 277 icdrGdrylstgvf 290 +cdrGdrylstg+f lcl|NCBI__GCF_002151265.1:WP_086510266.1 281 VCDRGDRYLSTGLF 294 ************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (298 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: 00:00:00.00 # Mc/sec: 8.88 // [ok]
This GapMind analysis is from Apr 10 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