Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PP_0297 PP_0297 L-serine dehydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1013 (458 letters) >FitnessBrowser__Putida:PP_0297 Length = 458 Score = 706 bits (1822), Expect = 0.0 Identities = 349/458 (76%), Positives = 390/458 (85%) Query: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQHLLADVRRVEIRLYGSLSATGVG 60 MAISVFDLFK+G+GPSSSHTVGPMRA A F Q L ++ L V+R+E+RLYGSLSATG+G Sbjct: 1 MAISVFDLFKIGVGPSSSHTVGPMRAGALFVQGLRERGELERVKRIEVRLYGSLSATGIG 60 Query: 61 HATDRACVMGLMGEWPDSIDPNSIDSRIQTLRETGELSLAGKSTIAFNWQRDLLLLDESL 120 H TD A +MGLMGEWPD+IDP I RI LRET L L + I F W RD+LLLDE+L Sbjct: 61 HGTDNATIMGLMGEWPDAIDPTQIVPRIADLRETNTLQLDSRLPIEFVWARDMLLLDENL 120 Query: 121 PYHPNAMSLTAFGETGELFEQTYYSVGGGFIIEAAEAESGIAPASDVVLPYDFSSAAELL 180 PYHPNAM+L A GE GEL TYYSVGGGF+++AA+A SG+ A VLPYDF+SAAELL Sbjct: 121 PYHPNAMTLIAEGEQGELHRDTYYSVGGGFVVDAAQAASGVLDADQTVLPYDFNSAAELL 180 Query: 181 KLCNQHGLRVSELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLNVPR 240 +LC Q+ L VS+LMMANE+ WRS+ +IR GL +W M+ECV GL++EG LPGGLNV R Sbjct: 181 RLCKQNDLSVSQLMMANEKVWRSEEDIRAGLHKLWEAMQECVNNGLKYEGTLPGGLNVRR 240 Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 RAAKLHRSL EIGKPNVI ST+SAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV Sbjct: 241 RAAKLHRSLQEIGKPNVIGSTMSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 Query: 301 LHYYMKFNPDASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360 LHYYM+F+ + VV +FL AAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLA+ Sbjct: 301 LHYYMRFSDAVDESSVVDYFLAAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 360 Query: 361 ILGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420 +LGATP Q+ENAAEI LEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA QMALRGDG+ Sbjct: 361 VLGATPPQVENAAEIALEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAVQMALRGDGE 420 Query: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458 HFISLD+VIRTMRDTGADMHDKYKETSRGGLAVS +EC Sbjct: 421 HFISLDQVIRTMRDTGADMHDKYKETSRGGLAVSAIEC 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: 628 Number of extensions: 16 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 PP_0297 PP_0297 (L-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.3242.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-213 693.1 0.1 1e-212 692.9 0.1 1.0 1 lcl|FitnessBrowser__Putida:PP_0297 PP_0297 L-serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0297 PP_0297 L-serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 692.9 0.1 1e-212 1e-212 1 449 [. 3 454 .. 3 455 .. 0.97 Alignments for each domain: == domain 1 score: 692.9 bits; conditional E-value: 1e-212 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpe 75 isvfdlfkiG+GPssshtvGPm+a++ fv+ l+++g+le+vkr++v lyGsl++tG Gh+td+a ++Gl+Ge p+ lcl|FitnessBrowser__Putida:PP_0297 3 ISVFDLFKIGVGPSSSHTVGPMRAGALFVQGLRERGELERVKRIEVRLYGSLSATGIGHGTDNATIMGLMGEWPD 77 79************************************************************************* PP TIGR00720 76 evdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfi 150 +d ++i ++++++e+++l+l ++ i+f ++d+ + de+lp+h+n+++l a e+ l+++tyysvGGGf+ lcl|FitnessBrowser__Putida:PP_0297 78 AIDPTQIVPRIADLRETNTLQLDSRLPIEFVWARDMLLLDENLPYHPNAMTLIAEGEQ-GELHRDTYYSVGGGFV 151 ****************************************************998777.789************* PP TIGR00720 151 vdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeeciergl 223 vd +++ + +++ +py+f+saaell+lCk+++ls+s+++++nek++rsee++ra l ++w++m+ec+++gl lcl|FitnessBrowser__Putida:PP_0297 152 VDAAQAASGVLDADqtVLPYDFNSAAELLRLCKQNDLSVSQLMMANEKVWRSEEDIRAGLHKLWEAMQECVNNGL 226 **9988765544433389********************************************************* PP TIGR00720 224 kaegvlpGglkvkrraaslkrklkakeets..kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavl 296 k eg+lpGgl+v+rraa+l+r l++ + + +++++++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl lcl|FitnessBrowser__Putida:PP_0297 227 KYEGTLPGGLNVRRRAAKLHRSLQEIGKPNviGSTMSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVL 301 *************************9988877899**************************************** PP TIGR00720 297 ayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeia 371 +yy +f + + e +vv+++l+a+a+Gil+k+nasisgaevGCqgevG+ac+maaaglae+lg+tp qvenaaeia lcl|FitnessBrowser__Putida:PP_0297 302 HYYMRFSDAVDESSVVDYFLAAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAEVLGATPPQVENAAEIA 376 *************************************************************************** PP TIGR00720 372 mehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGl 446 +ehnlGltCdPvgGlvq+PCiernaiaavkaina ++al++dg++++sld+vi+tmr+tG+dm+ kykets+gGl lcl|FitnessBrowser__Putida:PP_0297 377 LEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAVQMALRGDGEHFISLDQVIRTMRDTGADMHDKYKETSRGGL 451 *************************************************************************** PP TIGR00720 447 avk 449 av+ lcl|FitnessBrowser__Putida:PP_0297 452 AVS 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.33 // [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