Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_053939388.1 WG78_RS18835 arginine/lysine/ornithine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >NCBI__GCF_001294205.1:WP_053939388.1 Length = 756 Score = 383 bits (984), Expect = e-110 Identities = 236/672 (35%), Positives = 361/672 (53%), Gaps = 35/672 (5%) Query: 75 NIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLYDREIEAAAKKYEDGVLPPFFK 132 +IPI++ T + + + + ++ I H + R I A+ Y D + PPFF+ Sbjct: 97 DIPIYLYGETRTARHIPNDVLRELHGFIHMHEDTPE-FVARHIIREARSYLDTLAPPFFR 155 Query: 133 ALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHE 192 AL Y + G+ + CPGH GG F KSP G+ F+ F+GEN+ R+D+CNA +LG LL H Sbjct: 156 ALTHYAQDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCNAVDELGQLLDHT 215 Query: 193 GPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALV 252 GP +E++AAR+FNAD +FV NGT+TSN I + VAPGD+V+ DRN HKS+ + A++ Sbjct: 216 GPVAASERNAARIFNADHLFFVTNGTSTSNKIVWNSTVAPGDIVVVDRNCHKSILH-AIM 274 Query: 253 QAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDP---EKAKAK---RPFRLAV 306 G PV+L +R+ YG IG I +F+ ++IR K+ +P EK +A +P R+ Sbjct: 275 MTGAVPVFLMPTRNHYGIIGPIPRSEFEPENIRRKML-ANPFCREKLEADPDVKP-RVLT 332 Query: 307 IQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLGPDDPG- 365 I TYDG +YN +++ + + + FD AW+ + F D +G P Sbjct: 333 ITQSTYDGIMYNVEEIKGLLDGKIETLHFDEAWLPHAAFHDFYGDYHA----IGEGRPRC 388 Query: 366 ----ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFYPLF 421 I TQSTHK AG SQASQI +D+ Q+ ++ FN AY+ +STSP Y + Sbjct: 389 KESMIFSTQSTHKLLAGLSQASQILVQDA----QENQLDRDIFNEAYLMHTSTSPQYAII 444 Query: 422 ATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKPWQDAD-TE 480 A+ D+ A M E G L ++L +++ R+ + K + K W AD T+ Sbjct: 445 ASCDVAAAMMEAPGGTALVEESLSEALDFRRAMRK----VDEEYGDSWWFKVWGPADLTD 500 Query: 481 KIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGIPAVILA 540 + + D W + G +WHGF A+ +DP K + TPG+++ G++ + GIPA I++ Sbjct: 501 EGLDHRDAWMLKAGEEWHGFGDVAEGFNMLDPIKATIITPGLNM-AGDFAETGIPASIVS 559 Query: 541 NYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEVLPRLYS 600 YL EHG++ EK L S L T T+ + + L+T + +F+ +APL +LP + Sbjct: 560 KYLAEHGVVIEKTGLYSFFILFTIGITKGRWNTLLTALQQFKDDYDKNAPLWRILPE-FV 618 Query: 601 EHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVELLKNNAK 660 + +YE ++ LCQ++H YK + EM+L P A+ P +A ++ + Sbjct: 619 QQFPQYERIGLRDLCQQIHGIYKARDVARLTTEMYLSDLVP--ALKPAKAFAKMAHREIE 676 Query: 661 LVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFLILEESINRFPGFAPEIQGV 720 VPL ++EG PYPPGI ++PGE + +Y E N FPGF I G+ Sbjct: 677 RVPLDELEGRITAVMLTPYPPGIPLLIPGEVFNHTIVQYLKFAREFNNNFPGFETYIHGL 736 Query: 721 YFEKENGKSVAY 732 KE G + AY Sbjct: 737 VAVKE-GNTTAY 747 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: 1291 Number of extensions: 54 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: 756 Length adjustment: 40 Effective length of query: 705 Effective length of database: 716 Effective search space: 504780 Effective search space used: 504780 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 24 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