Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_046156677.1 VL52_RS08800 arginine/lysine/ornithine decarboxylase
Query= BRENDA::H8ZI01 (721 letters) >NCBI__GCF_000971335.1:WP_046156677.1 Length = 752 Score = 371 bits (952), Expect = e-107 Identities = 228/672 (33%), Positives = 345/672 (51%), Gaps = 43/672 (6%) Query: 56 VPVFVISDDSS--RIQADLMEKIYHIIDLNNQYDEQLYDREIESAAAKYEDGVLPPFFKS 113 +PV++ + + I D++ +++ I ++ E R I A Y D + PPFF++ Sbjct: 96 IPVYLYGETRTARHIPNDILRELHGFIHMHEDTPE-FVARHIIREAKSYLDNLAPPFFRA 154 Query: 114 LKAYVERGNIQFDCPGHQGGQYFRKHPAGRQLYDFYGENVFRSDICNADVDLGDLLIHEG 173 L Y G+ + CPGH GG F K P G+ + F+GEN+ R+D+CNA +LG LL H G Sbjct: 155 LVDYAYDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCNAVDELGQLLDHTG 214 Query: 174 PAMDAEKHAAKVFNADKTYFVMNGTSTSNNVAVAAAVAPGDLVLFDRNNHKSIYNAALVK 233 P +E++AA++FNAD +FV NGTSTSN + + VA GD+VL DRN HKS + A++ Sbjct: 215 PVAASERNAARIFNADHLFFVTNGTSTSNKIVWHSCVAAGDIVLVDRNCHKSNLH-AIIM 273 Query: 234 DGGRPVYLETSRDPYGFIGGIYARDFDEDYIRKQAA----KVDPVKAKQKRPFRLAIIQL 289 G PV+L +R+ YG IG I +F D I+K+ + ++ + R R+ + Sbjct: 274 TGAIPVFLMPTRNHYGIIGPIPKSEFQPDTIKKKILANPFAREMLEQRPNRKPRILTLTQ 333 Query: 290 GTYDGTIYNAKQVVEKIGHLCDYILFDSAWVGYEQFIPMMRDSSPLLLDLGP-----EDP 344 TYDG +YN +++ + D + FD AW+ + F RD +G ED Sbjct: 334 STYDGILYNVEEIKGLLDGEVDTLHFDEAWLPHACFHDFYRDFHA----IGEGRPRCEDS 389 Query: 345 GILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYIDHKRFNNAYNQYASTSPFYPLFATL 404 + TQSTHK AG SQASQI +D Q R +D FN AY + STSP Y + A+ Sbjct: 390 LVFSTQSTHKLLAGISQASQILVQDP----QNRQLDTAWFNEAYLMHTSTSPQYSIIASC 445 Query: 405 DVNAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFVPPVVHGKNW-------EDA 457 DV A M E G+ L ++LV ++ R+ + K +G++W +D Sbjct: 446 DVAAAMMEQPGGQSLVEESLVEAMEFRRAMRK---------VDEEYGRDWWFSVWGPDDL 496 Query: 458 DTEKIVDDIDYWRFEKGAKWHGFDGYEDNQYFVDPNKFLLTTPGINVQTGEYEDFGIPAT 517 + I D D W +WHGF G ED +DP K + TPG++V G +E+ GIPA Sbjct: 497 SDDGICDQTD-WTLRPDERWHGFAGIEDGFNMLDPIKATVLTPGLDVD-GSFEEMGIPAA 554 Query: 518 ILANYLREHGIIPEKNDLNSILFLMTPAETPAKMNNLVSQIVKFESLVKADAPLEDVLPR 577 I+ YL EHG++ EK L S + T T + N L+S + +F+ + PL V+P Sbjct: 555 IVTKYLTEHGVVVEKTGLYSFFIMFTIGITKGRWNTLISLLQQFKDDFDKNQPLWRVMPE 614 Query: 578 LYAQNKDRYNGYTIKQLCQELHNFYKGNNAKEYQKEMFLADYFPEQKMTPFDANVELLHN 637 A+ +Y+ ++ LCQ +H Y ++ +++L+D E M P DA ++ H Sbjct: 615 FVAK-YPQYDRVGLQDLCQRIHGLYTKHDVARLTTDIYLSDM--EPAMRPADAFAKMAHR 671 Query: 638 NAKLVKLSDIGGETALEGALPYPPGIFCVAPGEKWTKVAQTYFMILEEGINRFPGFAPEI 697 + V + + G PYPPGI + PGE++ K Y + PGF ++ Sbjct: 672 EIERVPVDQLEGRVTAVLLTPYPPGIPLLIPGERFNKTIVDYLRFAQAFNRELPGFETDV 731 Query: 698 QG-VYFEQEDGK 708 G V E +D K Sbjct: 732 HGLVAVEVQDRK 743 Lambda K H 0.318 0.137 0.409 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: 1250 Number of extensions: 56 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: 721 Length of database: 752 Length adjustment: 40 Effective length of query: 681 Effective length of database: 712 Effective search space: 484872 Effective search space used: 484872 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