Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AO353_15500 AO353_15500 serine dehydratase
Query= reanno::pseudo3_N2E3:AO353_15500 (458 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15500 Length = 458 Score = 911 bits (2354), Expect = 0.0 Identities = 458/458 (100%), Positives = 458/458 (100%) Query: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG 60 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG Sbjct: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG 60 Query: 61 HATDRACVMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESL 120 HATDRACVMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESL Sbjct: 61 HATDRACVMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESL 120 Query: 121 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL 180 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL Sbjct: 121 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL 180 Query: 181 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR 240 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR Sbjct: 181 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR 240 Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV Sbjct: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 Query: 301 LHYYMKFNPDASDDDVVAFFLAAASVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360 LHYYMKFNPDASDDDVVAFFLAAASVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD Sbjct: 301 LHYYMKFNPDASDDDVVAFFLAAASVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360 Query: 361 VLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420 VLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK Sbjct: 361 VLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420 Query: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC Sbjct: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458 Lambda K H 0.319 0.134 0.399 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: 797 Number of extensions: 14 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: 458 Length of database: 458 Length adjustment: 33 Effective length of query: 425 Effective length of database: 425 Effective search space: 180625 Effective search space used: 180625 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 (21.8 bits) S2: 51 (24.3 bits)
Align candidate AO353_15500 AO353_15500 (serine dehydratase)
to HMM TIGR00720 (L-serine ammonia-lyase (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/TIGR00720.hmm # target sequence database: /tmp/gapView.23429.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00720 [M=450] Accession: TIGR00720 Description: sda_mono: L-serine ammonia-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-213 695.6 0.0 1.8e-213 695.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 AO353_15500 serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 AO353_15500 serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 695.4 0.0 1.8e-213 1.8e-213 1 448 [. 3 453 .. 3 455 .. 0.98 Alignments for each domain: == domain 1 score: 695.4 bits; conditional E-value: 1.8e-213 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkav 65 isvfdlfk+GiGPssshtvGPm+aa++f+++l ++g leq++rv+v lyGsl++tG Gh+td+a lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 3 ISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVGHATDRAC 67 79*************************************************************** PP TIGR00720 66 llGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkay 130 ++Gl+Ge p+++d i ++++++e+++l la++ +i fd ++dl + de+lp+h+n+++l+a+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 68 VMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESLPYHPNAMSLTAF 132 ***************************************************************** PP TIGR00720 131 deegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvle 193 e+ +l e+tyysvGGGfiv+ +e+++ ++ +py+f+sa ell+lC+++gl +se++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 133 GES-GQLWEQTYYSVGGGFIVEAAEAESGVPASSdvVLPYEFSSAVELLSLCNQHGLRVSELMMA 196 *99.6799*************98887776655543388*************************** PP TIGR00720 194 nekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets..kdp 256 ne a+rs++e+r+ ll+iw+vm+ec+e+gl++eg+lpGgl v+rraa+l+r l + + + +++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 197 NERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPRRAAKLHRSLLEIGKPNviSST 261 ******************************************************99888877999 PP TIGR00720 257 lavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagai 321 l++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl+yy kf+++as+++vv f+l+a+ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 262 LSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVLHYYMKFNPDASDDDVVAFFLAAASV 326 ***************************************************************** PP TIGR00720 322 GilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGl 386 Gil+k+nasisgaevGCqgevG+ac+maaagla++lg+tpeq+enaaei++ehnlGltCdPvgGl lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 327 GILCKKNASISGAEVGCQGEVGSACAMAAAGLADVLGATPEQLENAAEIGLEHNLGLTCDPVGGL 391 ***************************************************************** PP TIGR00720 387 vqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlav 448 vq+PCiernaiaavkaina+++al++dgk+++sld+vi+tmr+tG+dm+ kykets+gGlav lcl|FitnessBrowser__pseudo3_N2E3:AO353_15500 392 VQVPCIERNAIAAVKAINATQMALRGDGKHFISLDRVIRTMRDTGADMHDKYKETSRGGLAV 453 *************************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (450 nodes) Target sequences: 1 (458 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: 00:00:00.02 # Mc/sec: 10.14 // [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