Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AO353_07775 AO353_07775 serine dehydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1013 (458 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07775 Length = 458 Score = 719 bits (1857), Expect = 0.0 Identities = 355/458 (77%), Positives = 398/458 (86%) Query: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQHLLADVRRVEIRLYGSLSATGVG 60 MAISVFDLFK+GIGPSSSHTVGPMRAAA F ++L ++ LL V R+E++L+GSLSATG+G Sbjct: 1 MAISVFDLFKIGIGPSSSHTVGPMRAAALFVESLREKGLLEQVHRIEVQLFGSLSATGIG 60 Query: 61 HATDRACVMGLMGEWPDSIDPNSIDSRIQTLRETGELSLAGKSTIAFNWQRDLLLLDESL 120 H +D A +MGLMGEWPD+IDP+ I RI TLRET L L G+ + F W RD+ L+DE+L Sbjct: 61 HGSDNAVIMGLMGEWPDAIDPSQIGIRIDTLRETHTLLLDGRLPVPFIWARDMRLIDENL 120 Query: 121 PYHPNAMSLTAFGETGELFEQTYYSVGGGFIIEAAEAESGIAPASDVVLPYDFSSAAELL 180 P+HPNAM+L A GE EL TYYSVGGGF+++ A+A SG+ VLPYDFSSAAELL Sbjct: 121 PFHPNAMTLVAEGENAELHRDTYYSVGGGFVVDEAQASSGVVDLDSTVLPYDFSSAAELL 180 Query: 181 KLCNQHGLRVSELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLNVPR 240 LC +H LRV+ELMMANE+ WRS+ EIR GL+ +W M++CVEQGL+HEGILPGGLNV R Sbjct: 181 ALCKKHNLRVAELMMANEKVWRSEEEIRSGLMKLWRAMQDCVEQGLKHEGILPGGLNVRR 240 Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 RAAKLHRSL E+ KPNVI STLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV Sbjct: 241 RAAKLHRSLQELNKPNVIGSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 Query: 301 LHYYMKFNPDASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360 LHY+MKF+ +D +VV +FLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLA+ Sbjct: 301 LHYFMKFSEAVTDANVVDYFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 360 Query: 361 ILGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420 ILGATPEQL NAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA QMALRGDG+ Sbjct: 361 ILGATPEQLCNAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQ 420 Query: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVS VEC Sbjct: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSAVEC 458 Lambda K H 0.319 0.134 0.396 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: 651 Number of extensions: 19 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_07775 AO353_07775 (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.5566.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-214 698.4 0.1 2.5e-214 698.2 0.1 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 AO353_07775 serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 AO353_07775 serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 698.2 0.1 2.5e-214 2.5e-214 1 449 [. 3 454 .. 3 455 .. 0.98 Alignments for each domain: == domain 1 score: 698.2 bits; conditional E-value: 2.5e-214 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkav 65 isvfdlfkiGiGPssshtvGPm+aa+ fve+l++kg leqv+r++v+l+Gsl++tG Gh++d+av lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 3 ISVFDLFKIGIGPSSSHTVGPMRAAALFVESLREKGLLEQVHRIEVQLFGSLSATGIGHGSDNAV 67 79*************************************************************** PP TIGR00720 66 llGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkay 130 ++Gl+Ge p+ +d +i ++++++e+++l l ++ + f ++d+++ de+lp+h+n+++l a lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 68 IMGLMGEWPDAIDPSQIGIRIDTLRETHTLLLDGRLPVPFIWARDMRLIDENLPFHPNAMTLVAE 132 **************************************************************998 PP TIGR00720 131 deegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvle 193 e+ + l+++tyysvGGGf+vde+++++ + + +py+f+saaell+lCk+++l ++e++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 133 GEN-AELHRDTYYSVGGGFVVDEAQASSGVVDLDstVLPYDFSSAAELLALCKKHNLRVAELMMA 196 777.99*******************9988877664478*************************** PP TIGR00720 194 nekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets..kdp 256 nek++rseee+r+ l+++w++m++c+e+glk+eg+lpGgl+v+rraa+l+r l++ ++ + ++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 197 NEKVWRSEEEIRSGLMKLWRAMQDCVEQGLKHEGILPGGLNVRRRAAKLHRSLQELNKPNviGST 261 *******************************************************9999877899 PP TIGR00720 257 lavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagai 321 l++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl+y+ kf e +++ +vv+++l a+a+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 262 LSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVLHYFMKFSEAVTDANVVDYFLGAAAV 326 ***************************************************************** PP TIGR00720 322 GilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGl 386 Gil+k+nasisgaevGCqgevG+ac+maaaglae+lg+tpeq++naaei++ehnlGltCdPvgGl lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 327 GILCKKNASISGAEVGCQGEVGSACAMAAAGLAEILGATPEQLCNAAEIGLEHNLGLTCDPVGGL 391 ***************************************************************** PP TIGR00720 387 vqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavk 449 vq+PCiernaiaavkainaa++al++dg++++sld+vi+tmr+tG+dm+ kykets+gGlav+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_07775 392 VQVPCIERNAIAAVKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHDKYKETSRGGLAVS 454 *************************************************************95 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: 10.00 // [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