Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate PfGW456L13_3776 Arginine decarboxylase (EC 4.1.1.19) / Ornithine decarboxylase (EC 4.1.1.17)
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3776 Length = 761 Score = 350 bits (898), Expect = e-100 Identities = 222/679 (32%), Positives = 333/679 (49%), Gaps = 30/679 (4%) Query: 65 IINKADETKFNIPIFIITDDSSKVDGETMSKIFHIID--WHNNYDRRLYDREIEAAAKKY 122 ++ K E +P+F+I+D ++ + + H D W R I AA ++Y Sbjct: 83 LLVKLRERNTRVPVFLISDRTT-ASSIPLLVMQHADDFIWLPEDTSRFLSGRILAAIERY 141 Query: 123 EDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICNAD 182 LPP F AL + + PGH GG F KS AGR FY F+GEN+ RSD+ + Sbjct: 142 RQAALPPMFGALVKFARNYEYSWHTPGHAGGTAFLKSTAGRAFYEFFGENLLRSDLSISV 201 Query: 183 VDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDRNN 242 +LG LL H GP E++AA+VF A +TY+V NG++ SN + + A+V + L DRN Sbjct: 202 GELGSLLDHSGPIGQGERYAAKVFGAHRTYYVTNGSSMSNRVILMASVTRNQIALCDRNC 261 Query: 243 HKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAKRPF 302 HKS + A+ +G P YL +R+ YG IG I + + ++ IA K Sbjct: 262 HKSAEH-AMTLSGAIPTYLVPTRNRYGIIGPILPQTLSAEGVKAAIANNPLVKQGIDPTP 320 Query: 303 RLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLGPD 362 A++ TYDG YN +V E +G D + FD AW GY +F P+ + N Sbjct: 321 VHAIVTNSTYDGLTYNVTRVEELLGESVDRLHFDEAWYGYARFNPLYSGRHAMHGNPADH 380 Query: 363 D---PGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFYP 419 D P + TQSTHK A SQAS IH +D + I H +FN +YM +STSP Y Sbjct: 381 DKSKPTVFATQSTHKLLAALSQASMIHVRDG-----RNPIEHARFNESYMMHASTSPNYA 435 Query: 420 LFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLL--------KNATMIKPFLPPVVH- 470 + A+ D+++ M E +G+ L ++++ +++ R+ L KN + PP V Sbjct: 436 IMASCDVSSAMMEAPSGQILTNESIEEAISFRQVLSRMHNEMVGKNDWFFTCWQPPTVQV 495 Query: 471 ---GKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETG 527 P+ + D + +D + W A WHGF D +DP K + +PG+ + G Sbjct: 496 GAAAVPFHEVDPATLKTDPNCWVLHPNAVWHGFGDIEDGYCMLDPIKVSVLSPGMG-DDG 554 Query: 528 EYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKA 587 GIPA ++ YL GI+ EK +ILFL + T+ K L+ ++ F+ Sbjct: 555 SLLASGIPACVVTAYLGRQGIVVEKTTDFTILFLFSIGITKGKWGTLLNALLDFKRDYDD 614 Query: 588 DAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTP 647 +A L+ LP LY+ +Q RY G +K L E+ K + T + F P+ +P Sbjct: 615 NAELELCLPDLYNANQHRYAGMGLKDLADEIFAAMKKHKTTANMSQAF--GTLPKAEFSP 672 Query: 648 YQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKV---AQKYFLILE 704 +A +L++N+ +LV L + G A G +PYPPGI ++PGE Y LE Sbjct: 673 VEAYEKLVRNDIELVTLNEAAGRLAATGIVPYPPGIPLLMPGENAGPADGPLLAYLKALE 732 Query: 705 ESINRFPGFAPEIQGVYFE 723 FPGF + G+ E Sbjct: 733 AFDKSFPGFTHDTHGIEVE 751 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: 1233 Number of extensions: 62 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: 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