Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 199509 SO0314 ornithine decarboxylase, inducible (NCBI ptt file)
Query= BRENDA::A4Q8H0 (720 letters) >FitnessBrowser__MR1:199509 Length = 720 Score = 1164 bits (3010), Expect = 0.0 Identities = 548/719 (76%), Positives = 630/719 (87%) Query: 1 MKKLKIAANEKTLGCFETEREIVDVHQSDFNDVAAIVLSVEDVAKGMVTHLEEIGLNIPL 60 MK LK+AA+ CF+ +RE+V+V +DF DV A V+SV+DV G+V ++ GL +P+ Sbjct: 1 MKSLKVAASLSVRSCFDIDREVVNVLTTDFCDVGAAVVSVDDVKDGIVEKIKNTGLKLPI 60 Query: 61 FVAVCCEEELDNAVLPALHGVFELCGKNTQFYGKQLEAAAVKYEKDLLPPFFNTLTQYVE 120 FV+VCCEE + + ++ GVFELCG NT FYGKQ+E A KYE+ LLPPFF TL +YVE Sbjct: 61 FVSVCCEETFPDDICSSITGVFELCGSNTDFYGKQVETAIKKYEQALLPPFFGTLKKYVE 120 Query: 121 MGNATFACPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCNADVKLGDLLIHEGLPCAAQ 180 MGN+TFACPGHQGG+FFRKHP GRQFFDF+GET+FRSDMCNADVKLGDLLIHEG P AQ Sbjct: 121 MGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETIFRSDMCNADVKLGDLLIHEGAPLDAQ 180 Query: 181 QHAAKVFNADKTYFVLNGTSASNKVATNALLTRGDLVLFDRNNHKSNHHGALIQAGATPV 240 ++AAKVFNADKTYFVLNGTS+SNKVATNALL +GDLVLFDRNNHKSNHHGALIQAGATP+ Sbjct: 181 KYAAKVFNADKTYFVLNGTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGALIQAGATPI 240 Query: 241 YLETARNPFGFIGGIDAHCFDERYLRQQIREVAPERANEARPFRLAIIQLGTYDGTIYNA 300 YLETARNPFGFIGGIDAHCF E YLR+QIREVAPERA+E RPFRLAIIQLGTYDGTIYNA Sbjct: 241 YLETARNPFGFIGGIDAHCFKEAYLREQIREVAPERADEKRPFRLAIIQLGTYDGTIYNA 300 Query: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELNENDPGIIVTQSVHKQQAGF 360 RQVVD+IGHLCDYILFDSAWVGYEQFIPMM DCSPLLLEL DPGIIVTQSVHKQQAGF Sbjct: 301 RQVVDRIGHLCDYILFDSAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGF 360 Query: 361 SQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHASTSPFYPLFAALDVNAKMHEGKSGQRL 420 SQTSQIHKKDKHIKGQ+RYCNHKRFNNAFM+HASTS FYPLFAALDVNAKMHEG SG+ L Sbjct: 361 SQTSQIHKKDKHIKGQARYCNHKRFNNAFMMHASTSHFYPLFAALDVNAKMHEGASGRYL 420 Query: 421 WKECVRVGIEARKMLLETCQLIKPFVPDQIDGKPWQSYDTETMANDLRFFNFVPGEKWHA 480 W+E V+ GIEARK+LL+ C+ IKPF+P IDG+ WQ Y TE MA+DLRFF F PG+KWH+ Sbjct: 421 WREAVKAGIEARKLLLKKCKYIKPFIPSMIDGRQWQDYPTEQMADDLRFFEFEPGQKWHS 480 Query: 481 FEGYAESQYFVDPCKLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSIL 540 FEGY + QYFVDPCK LLTTPGID +G Y++FGIPATILAN+LREN I+PEKCDLNSIL Sbjct: 481 FEGYEKGQYFVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSIL 540 Query: 541 FLLTPAEDIAKMQHLVALIARFEKHIEQDSLLSEVLPAVYKSNEQRYKNYTLRQLCQEMH 600 FL+TPAED+AKMQHLV+ I+RFEK +++D+ LSEVLP VY +N+ RYK+YT+RQLCQEMH Sbjct: 541 FLMTPAEDMAKMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMH 600 Query: 601 DLYVSYDVKELQKEMFRKNYFPRIAMNPQDANTEFVRGNIELVSLAKAEGRIAAEGALPY 660 +LYVS+DVK+LQKEMFR +FP M+PQ+AN EF+RGN+ELV L++ EGRIAAEGALPY Sbjct: 601 NLYVSHDVKQLQKEMFRHAHFPTKVMDPQEANLEFIRGNVELVPLSQIEGRIAAEGALPY 660 Query: 661 PPGVLCVVPGEIWGGAAQRYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYVMS 719 PPGVLC+VPGEIWGGA QRYFLALEEGINLLPGF+PELQGVY++ DG +A GYV++ Sbjct: 661 PPGVLCMVPGEIWGGAVQRYFLALEEGINLLPGFSPELQGVYLESTPDGKIQALGYVLN 719 Lambda K H 0.321 0.138 0.420 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: 1649 Number of extensions: 59 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: 720 Length of database: 720 Length adjustment: 40 Effective length of query: 680 Effective length of database: 680 Effective search space: 462400 Effective search space used: 462400 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 199509 SO0314 (ornithine decarboxylase, inducible (NCBI ptt file))
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.3398.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 1430.1 0.1 0 1429.9 0.1 1.0 1 lcl|FitnessBrowser__MR1:199509 SO0314 ornithine decarboxylase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199509 SO0314 ornithine decarboxylase, inducible (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1429.9 0.1 0 0 1 719 [] 1 719 [. 1 719 [. 1.00 Alignments for each domain: == domain 1 score: 1429.9 bits; conditional E-value: 0 TIGR04301 1 mkklkiavsesvkdafeterevveleetdftdvaavvlsvedvkagvlekieetafeipvfvvveeeekvsaellkkvt 79 mk+lk+a+s sv+++f+++revv++ +tdf+dv+a+v+sv+dvk g++eki++t++++p+fv v++ee++++++++++t lcl|FitnessBrowser__MR1:199509 1 MKSLKVAASLSVRSCFDIDREVVNVLTTDFCDVGAAVVSVDDVKDGIVEKIKNTGLKLPIFVSVCCEETFPDDICSSIT 79 99***************************************************************************** PP TIGR04301 80 gvidleekdaelygrqleeaakkyeekllppffkalkkyvekgnsafdcpghqggeffrkhpagrqfvdffgenlfrsd 158 gv++l+ +++++yg+q+e+a+kkye++llppff++lkkyve+gns+f+cpghqgg+ffrkhp+grqf+dffge++frsd lcl|FitnessBrowser__MR1:199509 80 GVFELCGSNTDFYGKQVETAIKKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETIFRSD 158 ******************************************************************************* PP TIGR04301 159 lcnadvalgdllihegaplaaqkhaakvfnadktyfvlngtsasnkvvlnallapgdlvlfdrnnhksnhhgallqaga 237 +cnadv+lgdllihegapl+aqk+aakvfnadktyfvlngts+snkv++nalla+gdlvlfdrnnhksnhhgal+qaga lcl|FitnessBrowser__MR1:199509 159 MCNADVKLGDLLIHEGAPLDAQKYAAKVFNADKTYFVLNGTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGALIQAGA 237 ******************************************************************************* PP TIGR04301 238 tpvyletarnpfgfiggidehcfeeeylrelirevaperakekrpfrlaviqlgtydgtiynarqvvdkighlcdyilf 316 tp+yletarnpfgfiggid+hcf+e+ylre+irevapera+ekrpfrla+iqlgtydgtiynarqvvd+ighlcdyilf lcl|FitnessBrowser__MR1:199509 238 TPIYLETARNPFGFIGGIDAHCFKEAYLREQIREVAPERADEKRPFRLAIIQLGTYDGTIYNARQVVDRIGHLCDYILF 316 ******************************************************************************* PP TIGR04301 317 dsawvgyeqfipmmkdcsplllelneedpgilvtqsvhkqqagfsqtsqihkkdkhikgqaryvnhkrlnnafmlhast 395 dsawvgyeqfipmm+dcsplllel++edpgi+vtqsvhkqqagfsqtsqihkkdkhikgqary+nhkr+nnafm+hast lcl|FitnessBrowser__MR1:199509 317 DSAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQARYCNHKRFNNAFMMHAST 395 ******************************************************************************* PP TIGR04301 396 spfyplfaaldvnaklhegeagkrlwadcvktgiearklllkscklikpfvpelvdgkkwedydteeiandlrffefep 474 s fyplfaaldvnak+heg++g+ lw+++vk+giearklllk+ck+ikpf+p+++dg++w+dy+te++a+dlrffefep lcl|FitnessBrowser__MR1:199509 396 SHFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLKKCKYIKPFIPSMIDGRQWQDYPTEQMADDLRFFEFEP 474 ******************************************************************************* PP TIGR04301 475 gekwhsfegyeeeqyfvdpcklllttpgidvetgeyeefgvpatilanflrengiipekcdlnsilflltpaedlaklq 553 g+kwhsfegye+ qyfvdpck+llttpgid+etg+y+efg+patilanflren+iipekcdlnsilfl+tpaed+ak+q lcl|FitnessBrowser__MR1:199509 475 GQKWHSFEGYEKGQYFVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDMAKMQ 553 ******************************************************************************* PP TIGR04301 554 elvaqiarfeklleedaplkevlpsvykaneerykgytirqlcqemhdlykernvkqlqkelfrkeylpkvvlnpqean 632 +lv+qi+rfekl++edapl+evlp+vy+an++ryk+ytirqlcqemh+ly++++vkqlqke+fr++++p++v++pqean lcl|FitnessBrowser__MR1:199509 554 HLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVKQLQKEMFRHAHFPTKVMDPQEAN 632 ******************************************************************************* PP TIGR04301 633 leflrgevelveleeaegriaaegalpyppgvlcvvpgevwggavlkyflaleeginllpgfapelqgvyleededgrk 711 lef+rg+velv+l+++egriaaegalpyppgvlc+vpge+wggav++yflaleeginllpgf+pelqgvyle++ dg+ lcl|FitnessBrowser__MR1:199509 633 LEFIRGNVELVPLSQIEGRIAAEGALPYPPGVLCMVPGEIWGGAVQRYFLALEEGINLLPGFSPELQGVYLESTPDGKI 711 ******************************************************************************* PP TIGR04301 712 raygyvlk 719 +a gyvl+ lcl|FitnessBrowser__MR1:199509 712 QALGYVLN 719 ******95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (719 nodes) Target sequences: 1 (720 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06 # Mc/sec: 8.14 // [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