Align ornithine decarboxylase, degradative (EC 4.1.1.17) (characterized)
to candidate 14824 b0693 ornithine decarboxylase isozyme, inducible (NCBI)
Query= ecocyc::ORNDECARBOXDEG-MONOMER (732 letters) >FitnessBrowser__Keio:14824 Length = 732 Score = 1503 bits (3891), Expect = 0.0 Identities = 732/732 (100%), Positives = 732/732 (100%) Query: 1 MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPV 60 MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPV Sbjct: 1 MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPV 60 Query: 61 FIATENQERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVN 120 FIATENQERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVN Sbjct: 61 FIATENQERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVN 120 Query: 121 QGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIHEGAPCIAQ 180 QGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIHEGAPCIAQ Sbjct: 121 QGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIHEGAPCIAQ 180 Query: 181 QHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGATPV 240 QHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGATPV Sbjct: 181 QHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGATPV 240 Query: 241 YLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNA 300 YLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNA Sbjct: 241 YLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNA 300 Query: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGF 360 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGF Sbjct: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGF 360 Query: 361 SQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMHEGVSGRNM 420 SQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMHEGVSGRNM Sbjct: 361 SQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMHEGVSGRNM 420 Query: 421 WMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVPGEHWHS 480 WMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVPGEHWHS Sbjct: 421 WMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVPGEHWHS 480 Query: 481 FEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSIL 540 FEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSIL Sbjct: 481 FEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSIL 540 Query: 541 FLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMH 600 FLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMH Sbjct: 541 FLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMH 600 Query: 601 DLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRLPDAEGRIAAEGALPY 660 DLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRLPDAEGRIAAEGALPY Sbjct: 601 DLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRLPDAEGRIAAEGALPY 660 Query: 661 PPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIEEHDGRKQVWCYVIKPR 720 PPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIEEHDGRKQVWCYVIKPR Sbjct: 661 PPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIEEHDGRKQVWCYVIKPR 720 Query: 721 DAQSTLLKGEKL 732 DAQSTLLKGEKL Sbjct: 721 DAQSTLLKGEKL 732 Lambda K H 0.322 0.138 0.424 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: 2060 Number of extensions: 61 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: 732 Length of database: 732 Length adjustment: 40 Effective length of query: 692 Effective length of database: 692 Effective search space: 478864 Effective search space used: 478864 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 (21.9 bits) S2: 55 (25.8 bits)
Align candidate 14824 b0693 (ornithine decarboxylase isozyme, inducible (NCBI))
to HMM TIGR04301 (speF: ornithine decarboxylase SpeF (EC 4.1.1.17))
# 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/TIGR04301.hmm # target sequence database: /tmp/gapView.6170.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04301 [M=719] Accession: TIGR04301 Description: ODC_inducible: ornithine decarboxylase SpeF 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1433.6 0.0 0 1433.4 0.0 1.0 1 lcl|FitnessBrowser__Keio:14824 b0693 ornithine decarboxylase is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14824 b0693 ornithine decarboxylase isozyme, inducible (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1433.4 0.0 0 0 1 719 [] 1 718 [. 1 718 [. 1.00 Alignments for each domain: == domain 1 score: 1433.4 bits; conditional E-value: 0 TIGR04301 1 mkklkiavsesvkdafeterevveleetdftdvaavvlsvedvkagvlekieetafeipvfvvveeeekvsaellkkvt 79 m+klkiavs+s+ d+f+t+re++ ++e++ +dvaa+vls++dv++g+l++i++t+++ipvf+++e++e+v+ae+l++++ lcl|FitnessBrowser__Keio:14824 1 MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPVFIATENQERVPAEYLPRIS 79 89***************************************************************************** PP TIGR04301 80 gvidleekdaelygrqleeaakkyeekllppffkalkkyvekgnsafdcpghqggeffrkhpagrqfvdffgenlfrsd 158 gv++++e+++e+ygrqle+aa++ye++l+ppff+al++yv++gnsafdcpghqggeffr+hpag+qfv++fge+lfr+d lcl|FitnessBrowser__Keio:14824 80 GVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVNQGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRAD 158 ******************************************************************************* PP TIGR04301 159 lcnadvalgdllihegaplaaqkhaakvfnadktyfvlngtsasnkvvlnallapgdlvlfdrnnhksnhhgallqaga 237 lcnadva+gdllihegap+ aq+haakvfnadktyfvlngts+snkvvlnall+pgdlvlfdrnnhksnhhgallqaga lcl|FitnessBrowser__Keio:14824 159 LCNADVAMGDLLIHEGAPCIAQQHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGA 237 ******************************************************************************* PP TIGR04301 238 tpvyletarnpfgfiggidehcfeeeylrelirevaperakekrpfrlaviqlgtydgtiynarqvvdkighlcdyilf 316 tpvyletarnp+gfiggid+hcfee+ylreli+evap+rake+rpfrlaviqlgtydgtiynarqvvdkighlcdyilf lcl|FitnessBrowser__Keio:14824 238 TPVYLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNARQVVDKIGHLCDYILF 316 ******************************************************************************* PP TIGR04301 317 dsawvgyeqfipmmkdcsplllelneedpgilvtqsvhkqqagfsqtsqihkkdkhikgqaryvnhkrlnnafmlhast 395 dsawvgyeqfipmm+dcsplll+lne+dpgilvtqsvhkqqagfsqtsqihkkd+hikgq+ryv+hkr+nnafm+hast lcl|FitnessBrowser__Keio:14824 317 DSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGFSQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHAST 395 ******************************************************************************* PP TIGR04301 396 spfyplfaaldvnaklhegeagkrlwadcvktgiearklllkscklikpfvpelvdgkkwedydteeiandlrffefep 474 spfyplfaal++nak+heg +g+++w+dcv +gi+arkl+l++c++i+pfvpelvdgk+w++y+t++ia dlrff+f+p lcl|FitnessBrowser__Keio:14824 396 SPFYPLFAALNINAKMHEGVSGRNMWMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVP 474 ******************************************************************************* PP TIGR04301 475 gekwhsfegyeeeqyfvdpcklllttpgidvetgeyeefgvpatilanflrengiipekcdlnsilflltpaedlaklq 553 ge+whsfegy+e+qyfvdpcklllttpgid+++geye fgvpatilanflreng++pekcdlnsilflltpaed+aklq lcl|FitnessBrowser__Keio:14824 475 GEHWHSFEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSILFLLTPAEDMAKLQ 553 ******************************************************************************* PP TIGR04301 554 elvaqiarfeklleedaplkevlpsvykaneerykgytirqlcqemhdlykernvkqlqkelfrkeylpkvvlnpqean 632 +lva ++rfeklle+dapl+evlps+yk++eery gyt+rqlcqemhdly+++nvkqlqke+frke++p+v++npqean lcl|FitnessBrowser__Keio:14824 554 QLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMHDLYARHNVKQLQKEMFRKEHFPRVSMNPQEAN 632 ******************************************************************************* PP TIGR04301 633 leflrgevelveleeaegriaaegalpyppgvlcvvpgevwggavlkyflaleeginllpgfapelqgvyleededgrk 711 +++lrgevelv+l +aegriaaegalpyppgvlcvvpge+wggavl+yf aleeginllpgfapelqgvy+e ++dgrk lcl|FitnessBrowser__Keio:14824 633 YAYLRGEVELVRLPDAEGRIAAEGALPYPPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIE-EHDGRK 710 ************************************************************************.9***** PP TIGR04301 712 raygyvlk 719 ++++yv+k lcl|FitnessBrowser__Keio:14824 711 QVWCYVIK 718 ******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (719 nodes) Target sequences: 1 (732 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 10.29 // [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