Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate Ac3H11_2914 Arginine decarboxylase (EC 4.1.1.19); Ornithine decarboxylase (EC 4.1.1.17); Lysine decarboxylase (EC 4.1.1.18)
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2914 Length = 761 Score = 365 bits (937), Expect = e-105 Identities = 223/629 (35%), Positives = 335/629 (53%), Gaps = 26/629 (4%) Query: 113 REIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGEN 172 R I AK Y + V PPFFKAL Y E G+ + CPGH GG F KSP G+ ++ FYGEN Sbjct: 134 RHIIREAKSYLESVQPPFFKALLDYAEDGSYSWHCPGHSGGVAFLKSPVGQMYHQFYGEN 193 Query: 173 IFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAP 232 + R+D+CNA +LG LL H G ++E++AAR+FNAD +FV NGT+TSN + VAP Sbjct: 194 MLRADVCNAVEELGQLLDHNGAIGESERNAARIFNADHCFFVTNGTSTSNKMVWHHTVAP 253 Query: 233 GDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVD 292 GD+V+ DRN HKS+ + +++ G PV+++ +R+ +G IG I +F+ +I+ KI K + Sbjct: 254 GDVVVVDRNCHKSILH-SIIMTGAIPVFMKPTRNHFGIIGPIPQSEFEPAAIQAKI-KAN 311 Query: 293 P----EKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPM 348 P AK +P R+ + TYDG +YN + + + D + FD AW+ + F P Sbjct: 312 PLLKGVDAKKVKP-RVLTLTQSTYDGVLYNTETIKGMLDGYVDNLHFDEAWLPHAAFHPF 370 Query: 349 MKDSSPL-LLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNA 407 + P TQS HK AG SQAS + +DS R++ FN A Sbjct: 371 YGSYHAMGKKRTRPKYSVTYATQSIHKLLAGISQASHVLVQDSQTAKLDRHL----FNEA 426 Query: 408 YMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLL-------KNATM 460 Y+ +STSP Y + A+ D+ A M E G L ++L+ +++ R+ + KN Sbjct: 427 YLMHTSTSPQYSIIASCDVAAAMMEPPGGTALVEESLLEALDFRRAMRQVEEDFGKNDWW 486 Query: 461 IKPFLPPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTP 520 K + P + + A+ I SD K G+KWHGF AD +DP K + TP Sbjct: 487 FKVWGPDKLVDEGLGRAEDWIIRSDGKGKK--NGSKWHGFGQLADGFNMLDPIKSTIVTP 544 Query: 521 GIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVK 580 G++++ G+++ GIPA I+ YL EHG++ EK L S + T T+ + + L+T + + Sbjct: 545 GLNLD-GKFDKTGIPASIVTKYLAEHGVVVEKTGLYSFFIMFTIGITKGRWNTLLTALQQ 603 Query: 581 FESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYF 640 F+ + + P+ +LP +H+ RYE ++ LCQ VH+ Y + EM+L Sbjct: 604 FKDDYEKNQPMWRILPEFCQQHK-RYERMGLRDLCQHVHEMYAKYDIARLTTEMYLSDLT 662 Query: 641 PEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYF 700 P AM P A + + V + ++EG + PYPPGI ++PGE + K Y Sbjct: 663 P--AMKPSDAYAHIAHRTTERVEIDNLEGRITVGLVTPYPPGIPLLIPGEVFNKKIVDYL 720 Query: 701 LILEESINRFPGFAPEIQG-VYFEKENGK 728 E PGF +I G V E E+G+ Sbjct: 721 KFAREFAKLCPGFETDIHGLVEVEDESGQ 749 Lambda K H 0.318 0.136 0.405 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: 1324 Number of extensions: 61 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 745 Length of database: 761 Length adjustment: 40 Effective length of query: 705 Effective length of database: 721 Effective search space: 508305 Effective search space used: 508305 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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