Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate GFF1001 PS417_05075 serine dehydratase
Query= reanno::pseudo3_N2E3:AO353_15500 (458 letters) >FitnessBrowser__WCS417:GFF1001 Length = 458 Score = 835 bits (2157), Expect = 0.0 Identities = 420/458 (91%), Positives = 437/458 (95%) Query: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG 60 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQAL DQ LL QTRRVEVRLYGSLSATGVG Sbjct: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQQLLSQTRRVEVRLYGSLSATGVG 60 Query: 61 HATDRACVMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESL 120 HATDRACVMGLMGEWPD +DP+ I RIQQLRESG LLLAG + IAF+WQ+DL LLDESL Sbjct: 61 HATDRACVMGLMGEWPDRVDPTSINARIQQLRESGRLLLAGLQDIAFNWQQDLRLLDESL 120 Query: 121 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL 180 PYHPNAMSL A+GE+G L EQTYYSVGGGFI+EAAEA SG+ +SDV LPY+FSSAVELL Sbjct: 121 PYHPNAMSLHAYGENGLLSEQTYYSVGGGFIIEAAEAASGIAPTSDVQLPYDFSSAVELL 180 Query: 181 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR 240 +LCN+HGLRVSELMMANERAWRSDA+IRSGLLHIWSVMRECVEQGLR EGILPGGLDVPR Sbjct: 181 ALCNKHGLRVSELMMANERAWRSDADIRSGLLHIWSVMRECVEQGLRDEGILPGGLDVPR 240 Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 RAAKLHRSLLEIGKPNVI+STLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV Sbjct: 241 RAAKLHRSLLEIGKPNVITSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 Query: 301 LHYYMKFNPDASDDDVVAFFLAAASVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360 LHYYMKFN +ASDDDVV FFLAAA+VGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD Sbjct: 301 LHYYMKFNAEASDDDVVNFFLAAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 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: 744 Number of extensions: 17 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 GFF1001 PS417_05075 (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.8063.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-215 699.6 0.0 1.1e-214 699.4 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF1001 PS417_05075 serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF1001 PS417_05075 serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 699.4 0.0 1.1e-214 1.1e-214 1 448 [. 3 453 .. 3 455 .. 0.98 Alignments for each domain: == domain 1 score: 699.4 bits; conditional E-value: 1.1e-214 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpe 75 isvfdlfk+GiGPssshtvGPm+aa++f+++l +++ l+q++rv+v lyGsl++tG Gh+td+a ++Gl+Ge p+ lcl|FitnessBrowser__WCS417:GFF1001 3 ISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQQLLSQTRRVEVRLYGSLSATGVGHATDRACVMGLMGEWPD 77 79************************************************************************* PP TIGR00720 76 evdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfi 150 +vd +si++++++++e+++l la+ ++i f+ ++dl++ de+lp+h+n+++l+ay e+ +l e+tyysvGGGfi lcl|FitnessBrowser__WCS417:GFF1001 78 RVDPTSINARIQQLRESGRLLLAGLQDIAFNWQQDLRLLDESLPYHPNAMSLHAYGEN-GLLSEQTYYSVGGGFI 151 *******************************************************999.89************** PP TIGR00720 151 vdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeeciergl 223 ++ +e+ + + ++ ++py+f+sa ell+lC+++gl +se++++ne a+rs++++r+ ll+iw+vm+ec+e+gl lcl|FitnessBrowser__WCS417:GFF1001 152 IEAAEAASGIAPTSdvQLPYDFSSAVELLALCNKHGLRVSELMMANERAWRSDADIRSGLLHIWSVMRECVEQGL 226 *98888776655544599********************************************************* PP TIGR00720 224 kaegvlpGglkvkrraaslkrklkakeets..kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavl 296 + eg+lpGgl v+rraa+l+r l + + + +++l++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl lcl|FitnessBrowser__WCS417:GFF1001 227 RDEGILPGGLDVPRRAAKLHRSLLEIGKPNviTSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVL 301 ************************99888877899**************************************** PP TIGR00720 297 ayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeia 371 +yy kf+ eas+++vv+f+l+a+a+Gil+k+nasisgaevGCqgevG+ac+maaagla++lg+tpeq+enaaei+ lcl|FitnessBrowser__WCS417:GFF1001 302 HYYMKFNAEASDDDVVNFFLAAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLADVLGATPEQLENAAEIG 376 *************************************************************************** PP TIGR00720 372 mehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGl 446 +ehnlGltCdPvgGlvq+PCiernaiaavkaina+++al++dgk+++sld+vi+tmr+tG+dm+ kykets+gGl lcl|FitnessBrowser__WCS417:GFF1001 377 LEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGKHFISLDRVIRTMRDTGADMHDKYKETSRGGL 451 *************************************************************************** PP TIGR00720 447 av 448 av lcl|FitnessBrowser__WCS417:GFF1001 452 AV 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: 00:00:00.01 # Mc/sec: 11.65 // [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