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 BPHYT_RS14845 BPHYT_RS14845 cysteine synthase
Query= BRENDA::P29848 (303 letters) >FitnessBrowser__BFirm:BPHYT_RS14845 Length = 300 Score = 361 bits (927), Expect = e-104 Identities = 186/294 (63%), Positives = 219/294 (74%), Gaps = 4/294 (1%) Query: 3 TLEQTIGNTPLVKLQRLGPDN----GSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEI 58 T+E TIGNTPLV+L RL D + I KLEGNNPAGSVKDR ALSMI +AE RG I Sbjct: 5 TIEDTIGNTPLVQLVRLPDDEIRSRNNVILAKLEGNNPAGSVKDRPALSMIKKAEARGRI 64 Query: 59 KPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQG 118 KPGD LIE+TSGNTGIALAM AA++GY+M L+MP+++S ERR +M AYGA+++L G Sbjct: 65 KPGDTLIESTSGNTGIALAMAAAIRGYKMVLIMPEDLSVERRQSMAAYGAQIVLTPVTGG 124 Query: 119 MEGARDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGT 178 ME ARDLA M G+G +LDQF NPDNP AH TGPEIWR T GRITHFVSSMGTTGT Sbjct: 125 MEYARDLAEQMQREGKGIILDQFANPDNPAAHVEGTGPEIWRDTEGRITHFVSSMGTTGT 184 Query: 179 ITGVSRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAE 238 I GVS +L+EQ + + I+G QPEEGS IPGIR+WP Y+P IF+ S VD V ++ Q AE Sbjct: 185 IMGVSSYLKEQNQAIEIIGAQPEEGSRIPGIRKWPEAYLPKIFDRSRVDRVENVSQAAAE 244 Query: 239 NTMRELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVF 292 R +A EGIF G+SSGGA ALR+AR A +V I+CDRGDRYLSTGVF Sbjct: 245 AMARRMASVEGIFAGISSGGACEVALRIARQVENATIVFIVCDRGDRYLSTGVF 298 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: 314 Number of extensions: 10 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: 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 BPHYT_RS14845 BPHYT_RS14845 (cysteine synthase)
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.22735.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-137 442.4 0.4 4.8e-137 442.2 0.4 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS14845 BPHYT_RS14845 cysteine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS14845 BPHYT_RS14845 cysteine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.2 0.4 4.8e-137 4.8e-137 1 290 [] 5 298 .. 5 298 .. 0.99 Alignments for each domain: == domain 1 score: 442.2 bits; conditional E-value: 4.8e-137 TIGR01138 1 tilklvGntplvrlkrllpe....edsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieat 66 ti++++Gntplv+l rl+ + ++ +l+klegnnpaGsvkdrpalsmi +ae rG ik+Gd+lie+t lcl|FitnessBrowser__BFirm:BPHYT_RS14845 5 TIEDTIGNTPLVQLVRLPDDeirsRNNVILAKLEGNNPAGSVKDRPALSMIKKAEARGRIKPGDTLIEST 74 89****************99888778999***************************************** PP TIGR01138 67 sGntGialamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeekll 136 sGntGialam+aa++Gyk+ l+mp++ s er++ + ayGa+++l+ Gme ardla++++r+g++ +l lcl|FitnessBrowser__BFirm:BPHYT_RS14845 75 SGNTGIALAMAAAIRGYKMVLIMPEDLSVERRQSMAAYGAQIVLTPVTGGMEYARDLAEQMQREGKGIIL 144 ********************************************************************** PP TIGR01138 137 dqfnnpdnpkahytstGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieG 206 dqf+npdnp ah tG+eiw+ t+Grithfvss+GttGtimGvs +lkeqn+a++i+G qp+egs i+G lcl|FitnessBrowser__BFirm:BPHYT_RS14845 145 DQFANPDNPAAHVEGTGPEIWRDTEGRITHFVSSMGTTGTIMGVSSYLKEQNQAIEIIGAQPEEGSRIPG 214 ********************************************************************** PP TIGR01138 207 lrrieseylpgifdaslvdrvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvai 276 +r++++ ylp+ifd s+vdrv +v q ae +ar++a egif G+ssGga alr+ar++e+a +v i lcl|FitnessBrowser__BFirm:BPHYT_RS14845 215 IRKWPEAYLPKIFDRSRVDRVENVSQAAAEAMARRMASVEGIFAGISSGGACEVALRIARQVENATIVFI 284 ********************************************************************** PP TIGR01138 277 icdrGdrylstgvf 290 +cdrGdrylstgvf lcl|FitnessBrowser__BFirm:BPHYT_RS14845 285 VCDRGDRYLSTGVF 298 *************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.95 // [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