Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BWI76_RS24175 BWI76_RS24175 ornithine decarboxylase
Query= BRENDA::P21169 (711 letters) >FitnessBrowser__Koxy:BWI76_RS24175 Length = 712 Score = 1271 bits (3290), Expect = 0.0 Identities = 609/711 (85%), Positives = 665/711 (93%) Query: 1 MKSMNIAASSELVSRLSSHRRVVALGDTDFTDVAAVVITAADSRSGILALLKRTGFHLPV 60 MKSM+IAAS ELVSRLS+HRRVVAL TDFTDVAAVVIT ADSRSGILALLKRTGF+LPV Sbjct: 1 MKSMHIAASRELVSRLSTHRRVVALDSTDFTDVAAVVITVADSRSGILALLKRTGFNLPV 60 Query: 61 FLYSEHAVELPAGVTAVINGNEQQWLELESAACQYEENLLPPFYDTLTQYVEMGNSTFAC 120 +L+SE E P GV A+++G EQ+WLELE+AAC YEENLLPPF+DTLTQYVEM NSTFAC Sbjct: 61 YLFSEADHEKPQGVMAIVSGKEQEWLELEAAACGYEENLLPPFFDTLTQYVEMDNSTFAC 120 Query: 121 PGHQHGAFFKKHPAGRHFYDFFGENVFRADMCNADVKLGDLLIHEGSAKDAQKFAAKVFH 180 PGHQHGAFFKKHPAGR F+DFFGENVFRADMCNADVKLGDLLIHEGSAK AQKFAAKVF+ Sbjct: 121 PGHQHGAFFKKHPAGRQFFDFFGENVFRADMCNADVKLGDLLIHEGSAKHAQKFAAKVFN 180 Query: 181 ADKTYFVLNGTSAANKVVTNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLEASRNP 240 ADKTYFVLNGTSAANKVVTNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLEASRNP Sbjct: 181 ADKTYFVLNGTSAANKVVTNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLEASRNP 240 Query: 241 FGFIGGIDAHCFNEEYLRQQIRDVAPEKADLPRPYRLAIIQLGTYDGTVYNARQVIDTVG 300 FGFIGGID CF+E+YLR IR+ APEKAD+PRP+RLA+IQLGTYDGTVYNARQV+D +G Sbjct: 241 FGFIGGIDDRCFDEKYLRDLIRETAPEKADMPRPFRLAVIQLGTYDGTVYNARQVVDKIG 300 Query: 301 HLCDYILFDSAWVGYEQFIPMMADSSPLLLELNENDPGIFVTQSVHKQQAGFSQTSQIHK 360 LCDYILFDSAWVGYEQFIPMMAD SPLLL+L +DPGIFVTQSVHKQQAGFSQTSQIHK Sbjct: 301 SLCDYILFDSAWVGYEQFIPMMADCSPLLLDLTPDDPGIFVTQSVHKQQAGFSQTSQIHK 360 Query: 361 KDNHIRGQARFCPHKRLNNAFMLHASTSPFYPLFAALDVNAKIHEGESGRRLWAECVEIG 420 KDNH+RGQ RFCPHKRLNNAFMLHASTSPFYPLFAALDVNAKIHEGESGRRLWAECV +G Sbjct: 361 KDNHLRGQERFCPHKRLNNAFMLHASTSPFYPLFAALDVNAKIHEGESGRRLWAECVALG 420 Query: 421 IEARKAILARCKLFRPFIPPVVDGKLWQDYPTSVLASDRRFFSFEPGAKWHGFEGYAADQ 480 IEARKAI+A CK+ +PFIPPVV G+ WQD+PT +A +RRFFSFEPGA+WHGFEGYA+DQ Sbjct: 421 IEARKAIIANCKMIQPFIPPVVAGRPWQDHPTEAIARERRFFSFEPGARWHGFEGYASDQ 480 Query: 481 YFVDPCKLLLTTPGIDAETGEYSDFGVPATILAHYLRENGIVPEKCDLNSILFLLTPAES 540 YFVDPCKLLLTTPGIDAE+G+Y+DFG+PATILAHYLRENGIVPEKCDLNSILFLLTPAES Sbjct: 481 YFVDPCKLLLTTPGIDAESGKYTDFGIPATILAHYLRENGIVPEKCDLNSILFLLTPAES 540 Query: 541 HEKLAQLVAMLAQFEQHIEDDSPLVEVLPSVYNKYPVRYRDYTLRQLCQEMHDLYVSFDV 600 EKLAQLVAMLA+FEQHIE D+PL +VLP+++NKYPVRYRDYT+R+LCQEMH+LYVSFDV Sbjct: 541 AEKLAQLVAMLARFEQHIESDTPLADVLPTIFNKYPVRYRDYTIRELCQEMHNLYVSFDV 600 Query: 601 KDLQKAMFRQQSFPSVVMNPQDAHSAYIRGDVELVRIRDAEGRIAAEGALPYPPGVLCVV 660 KDLQK MFR++SFP VMNPQDA+ +IRG+VELVR+ AEGRIAAEGALPYPPGVLCVV Sbjct: 601 KDLQKEMFRKKSFPRAVMNPQDANREFIRGNVELVRLSAAEGRIAAEGALPYPPGVLCVV 660 Query: 661 PGEVWGGAVQRYFLALEEGVNLLPGFSPELQGVYSETDADGVKRLYGYVLK 711 PGE+WGGAV RYFLALEEGVN+LPGFSPELQGVYSETD DG+KRLYGYVLK Sbjct: 661 PGEIWGGAVLRYFLALEEGVNMLPGFSPELQGVYSETDPDGIKRLYGYVLK 711 Lambda K H 0.322 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: 1684 Number of extensions: 53 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: 711 Length of database: 712 Length adjustment: 39 Effective length of query: 672 Effective length of database: 673 Effective search space: 452256 Effective search space used: 452256 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)
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