Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AO353_03505 AO353_03505 serine dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5557 (458 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03505 Length = 458 Score = 864 bits (2232), Expect = 0.0 Identities = 431/458 (94%), Positives = 445/458 (97%) Query: 1 MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60 MSLSVFDLFKIGIGPSSSHTVGPMRAAARF EGLRR++LL TT VKVELYGSLGATGKG Sbjct: 1 MSLSVFDLFKIGIGPSSSHTVGPMRAAARFVEGLRRENLLAATTCVKVELYGSLGATGKG 60 Query: 61 HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIRKPL 120 HGSDKAVLLGLEGEHPDTV+TE + ARL IRSSGRLNLLGEH IEFNEKLHLAMIRKPL Sbjct: 61 HGSDKAVLLGLEGEHPDTVNTENIAARLNEIRSSGRLNLLGEHVIEFNEKLHLAMIRKPL 120 Query: 121 AFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKDL 180 A+HPNGMIFRAFDAAG+Q+RSREYYSVGGGFVVDE AAGADRIVED TPLTFPFKSAKDL Sbjct: 121 AYHPNGMIFRAFDAAGIQIRSREYYSVGGGFVVDEDAAGADRIVEDTTPLTFPFKSAKDL 180 Query: 181 LGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240 LGHC+TYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK Sbjct: 181 LGHCATYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVK 240 Query: 241 RRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPAV 300 RRAAALHRQLCKNPE++LRDPLSVLDWVNLYALAVNEENA GGRVVTAPTNGAAGI+PAV Sbjct: 241 RRAAALHRQLCKNPESSLRDPLSVLDWVNLYALAVNEENANGGRVVTAPTNGAAGIVPAV 300 Query: 301 LHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360 LHYYMRFIPGA+EDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE Sbjct: 301 LHYYMRFIPGANEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALCE 360 Query: 361 VLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDGH 420 VLGG+VQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMA+RGDG Sbjct: 361 VLGGTVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMALRGDGQ 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: 870 Number of extensions: 27 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_03505 AO353_03505 (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.27716.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-222 724.2 0.2 3.6e-222 724.0 0.2 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 AO353_03505 serine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 AO353_03505 serine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 724.0 0.2 3.6e-222 3.6e-222 2 450 .] 4 455 .. 3 455 .. 0.98 Alignments for each domain: == domain 1 score: 724.0 bits; conditional E-value: 3.6e-222 TIGR00720 2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavl 66 svfdlfkiGiGPssshtvGPm+aa++fve l++++ l++++ vkv+lyGsl++tGkGh++dkavl lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 4 SVFDLFKIGIGPSSSHTVGPMRAAARFVEGLRRENLLAATTCVKVELYGSLGATGKGHGSDKAVL 68 9**************************************************************** PP TIGR00720 67 lGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkayd 131 lGleGe+p++v++e+i ++l+e++++++l+l++++ i+f+++ +la+ ++ l +h+ng+ ++a+d lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 69 LGLEGEHPDTVNTENIAARLNEIRSSGRLNLLGEHVIEFNEKLHLAMIRKPLAYHPNGMIFRAFD 133 ***************************************************************** PP TIGR00720 132 eegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlen 194 +g ++++++yysvGGGf+vde++++ ++ e+ +++pfksa++ll +C++ glsis+v+l+n lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 134 AAGIQIRSREYYSVGGGFVVDEDAAGADRIVEDttPLTFPFKSAKDLLGHCATYGLSISQVMLTN 198 ***********************9988876555337889************************** PP TIGR00720 195 ekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kdpla 258 e a+r+e+e+ra ll+iw+vm++c+ g+++eg+lpGglkvkrraa+l+r+l ++ e+s +dpl+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 199 ESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKVKRRAAALHRQLCKNPESSlRDPLS 263 ********************************************************9999***** PP TIGR00720 259 vldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGi 323 vldwvnlyalavneena GgrvvtaPtnGaagi+Pavl+yy +f++ a+e+ vvrfllta+aiGi lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 264 VLDWVNLYALAVNEENANGGRVVTAPTNGAAGIVPAVLHYYMRFIPGANEDGVVRFLLTAAAIGI 328 ***************************************************************** PP TIGR00720 324 lykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvq 388 lykenasisgaevGCqgevGvacsmaa++l+e+lggt++qvenaaei+mehnlGltCdP+gGlvq lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 329 LYKENASISGAEVGCQGEVGVACSMAAGALCEVLGGTVQQVENAAEIGMEHNLGLTCDPIGGLVQ 393 ***************************************************************** PP TIGR00720 389 iPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450 +PCierna+++vkaina r+al++dg+++vsldkvi+tmr+tG+dmk+kyket++gGlav++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03505 394 VPCIERNAMGSVKAINAVRMALRGDGQHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNI 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 11.30 // [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