Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 14332 b0186 lysine decarboxylase 2, constitutive (NCBI)
Query= BRENDA::P21169 (711 letters) >FitnessBrowser__Keio:14332 Length = 713 Score = 322 bits (825), Expect = 4e-92 Identities = 211/620 (34%), Positives = 311/620 (50%), Gaps = 44/620 (7%) Query: 94 QYEENLLPPFYDTLTQYVEMGNSTFACPGHQHGAFFKKHPAGRHFYDFFGENVFRADMCN 153 +Y +N+ PPF L YV+ TF PGH G ++K P G FYDFFG N +AD+ Sbjct: 123 EYLDNITPPFTKALFTYVKERKYTFCTPGHMGGTAYQKSPVGCLFYDFFGGNTLKADVSI 182 Query: 154 ADVKLGDLLIHEGSAKDAQKFAAKVFHADKTYFVLNGTSAANKVVTNALLTRGDLVLFDR 213 + +LG LL H G +A+++ A+ F A+++Y V NGTS +NK+V G +L DR Sbjct: 183 SVTELGSLLDHTGPHLEAEEYIARTFGAEQSYIVTNGTSTSNKIVGMYAAPSGSTLLIDR 242 Query: 214 NNHKSNHHGALIQAGATPVYLEASRNPFGFIGGIDAHCFNEEYLRQQIRDVAPEKADLPR 273 N HKS H L+ PV+L+ +RN G +GGI F + + +++ A +A P Sbjct: 243 NCHKSLAH-LLMMNDVVPVWLKPTRNALGILGGIPRREFTRDSIEEKV--AATTQAQWPV 299 Query: 274 PYRLAIIQLGTYDGTVYNARQVIDTVGHLCDYILFDSAWVGYEQFIPMMADSSPLLLELN 333 A+I TYDG +YN + T+ I FDSAWV Y F P+ S + E Sbjct: 300 H---AVITNSTYDGLLYNTDWIKQTLD--VPSIHFDSAWVPYTHFHPIYQGKSGMSGE-R 353 Query: 334 ENDPGIFVTQSVHKQQAGFSQTSQIHKKDNHIRGQARFCPHKRLNNAFMLHASTSPFYPL 393 IF TQS HK A SQ S IH K + + N AFM+H +TSP YP+ Sbjct: 354 VAGKVIFETQSTHKMLAALSQASLIHIKGEY--------DEEAFNEAFMMHTTTSPSYPI 405 Query: 394 FAALDVNAKIHEGESGRRLWAECVEIGIEARKAILARCK-----LFRPFIPPVVDGKLWQ 448 A+++ A + G G+RL VE + RK + + F + PP VD Sbjct: 406 VASVETAAAMLRGNPGKRLINRSVERALHFRKEVQRLREESDGWFFDIWQPPQVD----- 460 Query: 449 DYPTSVLASDRRFFSFEPGAKWHGFEGYAADQYFVDPCKLLLTTPGIDAETGEYSDFGVP 508 + + PG +WHGF AD F+DP K+ + TPG+D E G S+ G+P Sbjct: 461 ---------EAECWPVAPGEQWHGFNDADADHMFLDPVKVTILTPGMD-EQGNMSEEGIP 510 Query: 509 ATILAHYLRENGIVPEKCDLNSILFLLTPAESHEKLAQLVAMLAQFEQHIEDDSPLVEVL 568 A ++A +L E GIV EK ++LFL + K L+ L +F++ + + + +L Sbjct: 511 AALVAKFLDERGIVVEKTGPYNLLFLFSIGIDKTKAMGLLRGLTEFKRSYDLNLRIKNML 570 Query: 569 PSVYNKYPVRYRDYTLRQLCQEMHDLYVSFDVKDLQKAMFRQQSFPSVVMNPQDAHSAYI 628 P +Y + P YR+ ++ L Q +H L D+ L F + P ++M P A I Sbjct: 571 PDLYAEDPDFYRNMRIQDLAQGIHKLIRKHDLPGLMLRAF--DTLPEMIMTPHQAWQRQI 628 Query: 629 RGDVELVRIRDAEGRIAAEGALPYPPGVLCVVPGEVW---GGAVQRYFLALEEGVNLLPG 685 +G+VE + + GR++A LPYPPGV ++PGE+ V + L L PG Sbjct: 629 KGEVETIALEQLVGRVSANMILPYPPGVPLLMPGEMLTKESRTVLDFLLMLCSVGQHYPG 688 Query: 686 FSPELQGVYSETDADGVKRL 705 F ++ G ++ D DGV R+ Sbjct: 689 FETDIHG--AKQDEDGVYRV 706 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: 1215 Number of extensions: 66 Number of successful extensions: 9 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: 713 Length adjustment: 39 Effective length of query: 672 Effective length of database: 674 Effective search space: 452928 Effective search space used: 452928 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