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 16520 b2421 cysteine synthase B (O-acetylserine sulfhydrolase B) (NCBI)
Query= SwissProt::P16703 (303 letters) >FitnessBrowser__Keio:16520 Length = 303 Score = 602 bits (1553), Expect = e-177 Identities = 303/303 (100%), Positives = 303/303 (100%) Query: 1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKP 60 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKP Sbjct: 1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKP 60 Query: 61 GDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGME 120 GDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGME Sbjct: 61 GDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGME 120 Query: 121 GARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTIT 180 GARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTIT Sbjct: 121 GARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTIT 180 Query: 181 GVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENT 240 GVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENT Sbjct: 181 GVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENT 240 Query: 241 MRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEHFSQG 300 MRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEHFSQG Sbjct: 241 MRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEHFSQG 300 Query: 301 AGI 303 AGI Sbjct: 301 AGI 303 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: 509 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: 303 Length adjustment: 27 Effective length of query: 276 Effective length of database: 276 Effective search space: 76176 Effective search space used: 76176 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 16520 b2421 (cysteine synthase B (O-acetylserine sulfhydrolase B) (NCBI))
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.6311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-175 566.5 0.1 7.4e-175 566.3 0.1 1.0 1 lcl|FitnessBrowser__Keio:16520 b2421 cysteine synthase B (O-ace Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16520 b2421 cysteine synthase B (O-acetylserine sulfhydrolase B) (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 566.3 0.1 7.4e-175 7.4e-175 1 290 [] 3 292 .. 3 292 .. 1.00 Alignments for each domain: == domain 1 score: 566.3 bits; conditional E-value: 7.4e-175 TIGR01138 1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGialamvaa 79 t+++++Gntplv+l+r++p+++sev++klegnnpaGsvkdr+alsmiveaekrGeik+GdvlieatsGntGialam+aa lcl|FitnessBrowser__Keio:16520 3 TLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEATSGNTGIALAMIAA 81 899**************************************************************************** PP TIGR01138 80 lkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahytstGieiwq 158 lkGy++kllmpdn+s+er+aa++ayGaelilv+ke+GmeGardla e++++ge+klldqfnnpdnp+ahyt+tG+eiwq lcl|FitnessBrowser__Keio:16520 82 LKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQ 160 ******************************************************************************* PP TIGR01138 159 qtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslvdrvvdveqedaed 237 qt+Grithfvss+GttGti+Gvsrf++eq+++v+ivGlqp+egs+i+G+rr+++eylpgif+aslvd+v+d++q+dae+ lcl|FitnessBrowser__Keio:16520 161 QTGGRITHFVSSMGTTGTITGVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAEN 239 ******************************************************************************* PP TIGR01138 238 iarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290 ++rela++egif+GvssGgava+alr+a+++++avvvaiicdrGdrylstgvf lcl|FitnessBrowser__Keio:16520 240 TMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVF 292 ****************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (303 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: 6.28 // [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