Align Probable L-serine dehydratase, beta chain; SDH; EC 4.3.1.17; L-serine deaminase; L-SD (uncharacterized)
to candidate Echvi_2833 Echvi_2833 L-serine dehydratase, iron-sulfur-dependent, beta subunit
Query= curated2:O34635 (220 letters) >FitnessBrowser__Cola:Echvi_2833 Length = 225 Score = 171 bits (433), Expect = 1e-47 Identities = 91/217 (41%), Positives = 133/217 (61%), Gaps = 1/217 (0%) Query: 5 SVFDIIGPVMIGPSSSHTAGAARIGRVARSLFGREPERIIVSFYGSFAETYKGHGTDVAI 64 SVFD+IGPVMIGPSSSHTAG RI R A + G P+ +++FY SFA TY+GHG+D AI Sbjct: 6 SVFDMIGPVMIGPSSSHTAGVVRIARAAIKVLGGIPDDAVITFYNSFARTYEGHGSDKAI 65 Query: 65 IGGLLDFDTFDERIKTAIQIAEAKGIDIEFR-VEDAVPVHPNTAKITISDEKGELELTGI 123 IGGL+D T D RIK A ++AEA+G+ F+ V +A HPNT K+ ++ ++E+ G Sbjct: 66 IGGLMDLKTDDARIKQAFELAEARGLTYIFKSVGNASVFHPNTIKLNLTKGDRKVEVIGE 125 Query: 124 SIGGGKIEITELNGFELRLSGNHPAILVVHNDKFGTIAGVANVLAKFSINVGHMEVARKD 183 S+GGG I I ++GF S +++ +D G IA + ++LA+ N+ M V+RK Sbjct: 126 SLGGGLINIKSIDGFHAEFSAQEHTLIIKADDVSGAIAFITSILAQEQANIATMSVSRKG 185 Query: 184 IGQLALMTIEVDQNIDDHILDELSKLPNIIQVTKIAD 220 +A IE+D ++ + L + I ++ I D Sbjct: 186 KRDMACHVIEMDSGLNAITIKYLESISWIHELIYIPD 222 Lambda K H 0.319 0.140 0.390 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: 144 Number of extensions: 5 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: 220 Length of database: 225 Length adjustment: 22 Effective length of query: 198 Effective length of database: 203 Effective search space: 40194 Effective search space used: 40194 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
Align candidate Echvi_2833 Echvi_2833 (L-serine dehydratase, iron-sulfur-dependent, beta subunit)
to HMM TIGR00719 (sdaAB: L-serine dehydratase, iron-sulfur-dependent, beta subunit (EC 4.3.1.17))
# 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.carbon/TIGR00719.hmm # target sequence database: /tmp/gapView.14994.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00719 [M=208] Accession: TIGR00719 Description: sda_beta: L-serine dehydratase, iron-sulfur-dependent, beta subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-63 199.7 3.7 2.8e-63 199.4 3.7 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2833 Echvi_2833 L-serine dehydratase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2833 Echvi_2833 L-serine dehydratase, iron-sulfur-dependent, beta subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.4 3.7 2.8e-63 2.8e-63 3 201 .. 4 201 .. 1 207 [. 0.96 Alignments for each domain: == domain 1 score: 199.4 bits; conditional E-value: 2.8e-63 TIGR00719 3 drsvfeviGpvmvGpssshtaGaakiarvarslvsreyervivslyGsfaetykGhGtdvalvGGlldfetdde 76 + svf++iGpvm+GpssshtaG ++iar a +++ ++ ++++y sfa+ty GhG+d+a++GGl+d++tdd lcl|FitnessBrowser__Cola:Echvi_2833 4 KSSVFDMIGPVMIGPSSSHTAGVVRIARAAIKVLGGIPDDAVITFYNSFARTYEGHGSDKAIIGGLMDLKTDDA 77 569*********************************************************************** PP TIGR00719 77 riktaielakakGldiifrvedlvdnvhpnsvkivisdekGeeeeliGisiGGGkikivelnGielelrGeysa 150 rik a+ela+a+Gl +if+ + +hpn++k+ +++ + + e+iG s+GGG i+i ++G++ e++ + + lcl|FitnessBrowser__Cola:Echvi_2833 78 RIKQAFELAEARGLTYIFKSVGNASVFHPNTIKLNLTKGDRK-VEVIGESLGGGLINIKSIDGFHAEFSAQEHT 150 ******************99888888********99987776.99***************************** PP TIGR00719 151 illvynekrGviayvasllakseinveslevkkkdltqlvlltvevdknld 201 ++++ ++ G+ia+++s+la+ + n+ ++ v +k +++ +e+d l+ lcl|FitnessBrowser__Cola:Echvi_2833 151 LIIKADDVSGAIAFITSILAQEQANIATMSVSRKGKRDMACHVIEMDSGLN 201 ***********************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (208 nodes) Target sequences: 1 (225 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: 00:00:00.00 # Mc/sec: 7.02 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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