Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate BPHYT_RS25100 BPHYT_RS25100 serine dehydratase
Query= reanno::acidovorax_3H11:Ac3H11_929 (466 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS25100 BPHYT_RS25100 serine dehydratase Length = 464 Score = 632 bits (1630), Expect = 0.0 Identities = 326/473 (68%), Positives = 372/473 (78%), Gaps = 16/473 (3%) Query: 1 MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVG 60 M+VSVFDLFKIGIGPSSSHTVGPMIAA +FA H++ L V V V+LFGSL ATG G Sbjct: 1 MNVSVFDLFKIGIGPSSSHTVGPMIAACRFASHIEDANLLGFVRGVKVDLFGSLGATGKG 60 Query: 61 HGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSL 120 HGTDKAVLLGL G+ PD IDPD I P + IR + L LLG+HPV F E+EHL F RK + Sbjct: 61 HGTDKAVLLGLEGNLPDSIDPDLIEPRLQAIRVTKQLVLLGKHPVKFDEREHLGFFRKLM 120 Query: 121 P-------LHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVG 173 P +HPNGM F AFD G + +EYYSVGGGFV++ G+RV + AG + Sbjct: 121 PGAPGSGIVHPNGMRFQAFDENGQLLVEKEYYSVGGGFVVNREGDRV--NGVRAGAE--- 175 Query: 174 HAQGLPHPFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQR 233 +P+PFRTG +L+ C+ TGL+ AQ+ NE R EVR L+AIW+TM+ V+R Sbjct: 176 ----VPYPFRTGDDLMRVCRETGLSIAQITLRNECAARPEQEVREGLLAIWRTMSACVER 231 Query: 234 GCASTGTLPGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRV 293 GC G LPGPMHV+RRAA+L +L S E +LRDPLSMLDWVNLYAMAVNEENAAGGRV Sbjct: 232 GCKVRGELPGPMHVKRRAADLCGQLRSRSEESLRDPLSMLDWVNLYAMAVNEENAAGGRV 291 Query: 294 VTAPTNGAAGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQG 353 VTAPTNGAAGVIPAVLHYYV F+ +N++GI FLLTA AIGIIYKE AS+SGAEVGCQG Sbjct: 292 VTAPTNGAAGVIPAVLHYYVKFMHASNDEGIVNFLLTAAAIGIIYKETASISGAEVGCQG 351 Query: 354 EVGVACSMAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAI 413 EVGVACSMAA ALAAVMGG+P Q+ENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAI Sbjct: 352 EVGVACSMAAAALAAVMGGTPTQVENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAI 411 Query: 414 KAINAARMALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLAVNVVEC 466 KA+NAARMA++GDGQH VSLD VIKTM +TGADMK KYKETSRGGLAVNV+EC Sbjct: 412 KALNAARMAMKGDGQHYVSLDNVIKTMRETGADMKTKYKETSRGGLAVNVIEC 464 Lambda K H 0.319 0.134 0.398 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: 714 Number of extensions: 25 Number of successful extensions: 3 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: 466 Length of database: 464 Length adjustment: 33 Effective length of query: 433 Effective length of database: 431 Effective search space: 186623 Effective search space used: 186623 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 BPHYT_RS25100 BPHYT_RS25100 (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.13038.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-222 724.4 0.1 3.1e-222 724.2 0.1 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS25100 BPHYT_RS25100 serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS25100 BPHYT_RS25100 serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 724.2 0.1 3.1e-222 3.1e-222 1 450 [] 3 461 .. 3 461 .. 0.99 Alignments for each domain: == domain 1 score: 724.2 bits; conditional E-value: 3.1e-222 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGle 70 +svfdlfkiGiGPssshtvGPm aa++f++++++++ l v+ vkvdl+Gsl++tGkGh+tdkavllGle lcl|FitnessBrowser__BFirm:BPHYT_RS25100 3 VSVFDLFKIGIGPSSSHTVGPMIAACRFASHIEDANLLGFVRGVKVDLFGSLGATGKGHGTDKAVLLGLE 72 69******************************************************************** PP TIGR00720 71 Gelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlp.......lhenglrlkaydee 133 G+lp+++d + ie +l++++ +k+l l++++ +kfd++++l f ++ +p +h+ng+r++a+de+ lcl|FitnessBrowser__BFirm:BPHYT_RS25100 73 GNLPDSIDPDLIEPRLQAIRVTKQLVLLGKHPVKFDEREHLGFFRKLMPgapgsgiVHPNGMRFQAFDEN 142 *************************************************99999999************* PP TIGR00720 134 gevlkektyysvGGGfivdeeelkkeeeeee.evpypfksaaellelCkeeglsisevvlenekalrsee 202 g++l+ek+yysvGGGf+v++e + + ++ evpypf++ ++l++ C+e+glsi+++ l+ne+a+r+e+ lcl|FitnessBrowser__BFirm:BPHYT_RS25100 143 GQLLVEKEYYSVGGGFVVNREGDRVNGVRAGaEVPYPFRTGDDLMRVCRETGLSIAQITLRNECAARPEQ 212 *********************99999888777************************************** PP TIGR00720 203 evraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavn 271 evr+ ll+iw++m++c+erg+k g lpG+++vkrraa l +l++++e+s +dpl++ldwvnlya+avn lcl|FitnessBrowser__BFirm:BPHYT_RS25100 213 EVREGLLAIWRTMSACVERGCKVRGELPGPMHVKRRAADLCGQLRSRSEESlRDPLSMLDWVNLYAMAVN 282 **********************************************999999****************** PP TIGR00720 272 eenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqge 341 eenaaGgrvvtaPtnGaag+iPavl+yy kf++ +++e +v+fllta+aiGi+yke+asisgaevGCqge lcl|FitnessBrowser__BFirm:BPHYT_RS25100 283 EENAAGGRVVTAPTNGAAGVIPAVLHYYVKFMHASNDEGIVNFLLTAAAIGIIYKETASISGAEVGCQGE 352 ********************************************************************** PP TIGR00720 342 vGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalk 411 vGvacsmaaa+la+++ggtp+qvenaaei+mehnlG+tCdPvgGlvqiPCierna++a+ka+naar+a+k lcl|FitnessBrowser__BFirm:BPHYT_RS25100 353 VGVACSMAAAALAAVMGGTPTQVENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKALNAARMAMK 422 ********************************************************************** PP TIGR00720 412 edgkkkvsldkvietmretGkdmkakyketskgGlavkv 450 +dg+++vsld+vi+tmretG+dmk+kykets+gGlav+v lcl|FitnessBrowser__BFirm:BPHYT_RS25100 423 GDGQHYVSLDNVIKTMRETGADMKTKYKETSRGGLAVNV 461 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (450 nodes) Target sequences: 1 (464 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 7.17 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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