Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AO356_18165 AO356_18165 serine dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5557 (458 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18165 Length = 458 Score = 889 bits (2298), Expect = 0.0 Identities = 447/458 (97%), Positives = 452/458 (98%) Query: 1 MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60 MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLL TSVKVELYGSLGATGKG Sbjct: 1 MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLESITSVKVELYGSLGATGKG 60 Query: 61 HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIRKPL 120 HGSDKAVLLGLEGEHPDTVDTETV+ARLQ IRS+GRLNLLG H+IEFNEKLHLAMIRKPL Sbjct: 61 HGSDKAVLLGLEGEHPDTVDTETVNARLQEIRSNGRLNLLGAHAIEFNEKLHLAMIRKPL 120 Query: 121 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDL 180 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDE AAGADRIVEDATPLTFPFKSAKDL Sbjct: 121 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEDAAGADRIVEDATPLTFPFKSAKDL 180 Query: 181 LGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240 LGHC+TYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK Sbjct: 181 LGHCTTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240 Query: 241 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV 300 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV Sbjct: 241 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV 300 Query: 301 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE Sbjct: 301 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360 Query: 361 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH 420 VLGG+VQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH Sbjct: 361 VLGGTVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH 420 Query: 421 HFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458 HFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC Sbjct: 421 HFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458 Lambda K H 0.320 0.136 0.401 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: 882 Number of extensions: 28 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 AO356_18165 AO356_18165 (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.1094.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-221 722.4 0.1 1.3e-221 722.2 0.1 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 AO356_18165 serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 AO356_18165 serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 722.2 0.1 1.3e-221 1.3e-221 2 450 .] 4 455 .. 3 455 .. 0.99 Alignments for each domain: == domain 1 score: 722.2 bits; conditional E-value: 1.3e-221 TIGR00720 2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdka 64 svfdlfkiGiGPssshtvGPm+aa++f+e l++ + le++++vkv+lyGsl++tGkGh++dka lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 4 SVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLESITSVKVELYGSLGATGKGHGSDKA 66 9************************************************************** PP TIGR00720 65 vllGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrl 127 vllGleGe+p++vd+e+++++l+e++++++l+l++ + i+f+++ +la+ ++ l +h+ng+ + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 67 VLLGLEGEHPDTVDTETVNARLQEIRSNGRLNLLGAHAIEFNEKLHLAMIRKPLAFHPNGMIF 129 *************************************************************** PP TIGR00720 128 kaydeegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsis 188 +a+d +g ++++++yysvGGGf+vde++++ ++ e+ +++pfksa++ll +C++ glsis lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 130 RAFDAAGLQVRSREYYSVGGGFVVDEDAAGADRIVEDatPLTFPFKSAKDLLGHCTTYGLSIS 192 ***************************9998876666347889******************** PP TIGR00720 189 evvlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakee 251 +v+l+ne a+r+e+e+ra ll+iw+vm++c+ g+++eg+lpGglkvkrraa+l+r+l ++ e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 193 QVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVKRRAAALHRQLCKNPE 255 *************************************************************99 PP TIGR00720 252 ts.kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvr 313 + +dpl+vldwvnlyalavneena GgrvvtaPtnGaagiiPavl+yy +f++ ase+ vvr lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 256 AAlRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAVLHYYMRFIPGASEDGVVR 318 999************************************************************ PP TIGR00720 314 flltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnl 376 fllta+aiGilykenasisgaevGCqgevGvacsmaa++l+e+lggt++qvenaaei+mehnl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 319 FLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCEVLGGTVQQVENAAEIGMEHNL 381 *************************************************************** PP TIGR00720 377 GltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyk 439 GltCdP+gGlvq+PCierna+++vkaina r+a+++dg+++vsldkvi+tmr+tG+dmk+kyk lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 382 GLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGHHFVSLDKVIRTMRQTGADMKSKYK 444 *************************************************************** PP TIGR00720 440 etskgGlavkv 450 et++gGlav++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18165 445 ETARGGLAVNI 455 *********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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.75 // [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