Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PP_3144 PP_3144 L-serine dehydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1013 (458 letters) >FitnessBrowser__Putida:PP_3144 Length = 458 Score = 712 bits (1839), Expect = 0.0 Identities = 357/458 (77%), Positives = 398/458 (86%) Query: 1 MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALIDQHLLADVRRVEIRLYGSLSATGVG 60 MAISVFDLFK+GIGPSSSHTVGPMRAAATFAQAL +Q LLA V RV++RLYGSLSATGVG Sbjct: 1 MAISVFDLFKIGIGPSSSHTVGPMRAAATFAQALREQGLLAQVTRVQVRLYGSLSATGVG 60 Query: 61 HATDRACVMGLMGEWPDSIDPNSIDSRIQTLRETGELSLAGKSTIAFNWQRDLLLLDESL 120 HATDRAC++GLMG+WPD IDP++I+SRI + + L L G +AF++ RD+LLLDESL Sbjct: 61 HATDRACLLGLMGQWPDCIDPSTIESRIGQVLQEHCLMLDGSHPLAFDYGRDMLLLDESL 120 Query: 121 PYHPNAMSLTAFGETGELFEQTYYSVGGGFIIEAAEAESGIAPASDVVLPYDFSSAAELL 180 PYHPNAMSL A L QTY+SVGGGFI+E AE ++ + + V+LPY+F S A+LL Sbjct: 121 PYHPNAMSLEAMDGQRSLLSQTYFSVGGGFIVEQAEIDAPASEMNAVMLPYEFDSGAQLL 180 Query: 181 KLCNQHGLRVSELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLNVPR 240 LC H L V++LMMANE AWR +AE+R+GLL IW+ MRECV GLR+EGILPGGL+V R Sbjct: 181 VLCKAHNLSVAQLMMANECAWRPEAEVREGLLRIWAAMRECVANGLRNEGILPGGLHVKR 240 Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 RAA+LHRSL E+GKPNVI STL AMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV Sbjct: 241 RAARLHRSLQELGKPNVIGSTLGAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300 Query: 301 LHYYMKFNPDASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360 LHYYMKFNP+A D DVV F LGAAAVGILCKKNASISGAEVGCQGEVGSAC+MAAAGLA Sbjct: 301 LHYYMKFNPNACDADVVDFLLGAAAVGILCKKNASISGAEVGCQGEVGSACSMAAAGLAQ 360 Query: 361 ILGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420 +LGATP QLENAAEI LEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA QMALRGDG+ Sbjct: 361 VLGATPPQLENAAEIALEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAVQMALRGDGE 420 Query: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458 HFISLDRVIRTMRDTGADMH YKETSRGGLAV++VEC Sbjct: 421 HFISLDRVIRTMRDTGADMHANYKETSRGGLAVAFVEC 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: 11 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_3144 PP_3144 (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.25522.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-212 690.4 0.1 6.6e-212 690.2 0.1 1.0 1 lcl|FitnessBrowser__Putida:PP_3144 PP_3144 L-serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3144 PP_3144 L-serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 690.2 0.1 6.6e-212 6.6e-212 1 449 [. 3 454 .. 3 455 .. 0.98 Alignments for each domain: == domain 1 score: 690.2 bits; conditional E-value: 6.6e-212 TIGR00720 1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpe 75 isvfdlfkiGiGPssshtvGPm+aa++f+++l+++g l+qv+rv+v lyGsl++tG Gh+td+a llGl+G+ p+ lcl|FitnessBrowser__Putida:PP_3144 3 ISVFDLFKIGIGPSSSHTVGPMRAAATFAQALREQGLLAQVTRVQVRLYGSLSATGVGHATDRACLLGLMGQWPD 77 79************************************************************************* PP TIGR00720 76 evdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfi 150 +d +ie+++ +v++e+ l l +++ + fd+ +d+ + de+lp+h+n+++l+a+d++ + l ++ty+svGGGfi lcl|FitnessBrowser__Putida:PP_3144 78 CIDPSTIESRIGQVLQEHCLMLDGSHPLAFDYGRDMLLLDESLPYHPNAMSLEAMDGQ-RSLLSQTYFSVGGGFI 151 ********************************************************99.788899********** PP TIGR00720 151 vdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeeciergl 223 v+++e++ ++e + +py+f s a+ll lCk+++ls+++++++ne+a+r+e+evr+ ll+iw +m+ec+ +gl lcl|FitnessBrowser__Putida:PP_3144 152 VEQAEIDAPASEMNavMLPYEFDSGAQLLVLCKAHNLSVAQLMMANECAWRPEAEVREGLLRIWAAMRECVANGL 226 *****9988776665589********************************************************* PP TIGR00720 224 kaegvlpGglkvkrraaslkrklkakeets..kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavl 296 ++eg+lpGgl+vkrraa+l+r l++ + + ++l +++wvnl+alavneenaaGgr+vtaPtnGaagiiPavl lcl|FitnessBrowser__Putida:PP_3144 227 RNEGILPGGLHVKRRAARLHRSLQELGKPNviGSTLGAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAVL 301 *************************998886689999************************************** PP TIGR00720 297 ayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeia 371 +yy kf+++a + +vv+fll a+a+Gil+k+nasisgaevGCqgevG+acsmaaagla++lg+tp q+enaaeia lcl|FitnessBrowser__Putida:PP_3144 302 HYYMKFNPNACDADVVDFLLGAAAVGILCKKNASISGAEVGCQGEVGSACSMAAAGLAQVLGATPPQLENAAEIA 376 *************************************************************************** PP TIGR00720 372 mehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGl 446 +ehnlGltCdPvgGlvq+PCiernaiaavkaina ++al++dg++++sld+vi+tmr+tG+dm+a+ykets+gGl lcl|FitnessBrowser__Putida:PP_3144 377 LEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAVQMALRGDGEHFISLDRVIRTMRDTGADMHANYKETSRGGL 451 *************************************************************************** PP TIGR00720 447 avk 449 av+ lcl|FitnessBrowser__Putida:PP_3144 452 AVA 454 *96 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 6.77 // [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