Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_046156677.1 VL52_RS08800 arginine/lysine/ornithine decarboxylase
Query= BRENDA::E8X9U7 (756 letters) >NCBI__GCF_000971335.1:WP_046156677.1 Length = 752 Score = 528 bits (1360), Expect = e-154 Identities = 291/769 (37%), Positives = 439/769 (57%), Gaps = 41/769 (5%) Query: 4 VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63 ++I++ +F ++T G+ + LA A+ + ++VI TS+ D + + S Sbjct: 7 IVIIDEDFRSENT-SGSGIRELAAAMEAEGMSVIGYTSYGDLTSFAQQQSRAAGFILSID 65 Query: 64 MEQPDEHLSVRQLIGKLH-------ERQQNVPVFLLGDREKATASLDRDLLELVDEFAWI 116 E+ S ++ +G L+ R ++PV+L G+ A + D+L + F + Sbjct: 66 DEEFQTVDSAQESLGNLYGFVAEIRRRNPDIPVYLYGETRTAR-HIPNDILRELHGFIHM 124 Query: 117 LEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGR 176 EDT +F+A + Y L PP F AL+ Y+ YSW PGH GGV F K+P G+ Sbjct: 125 HEDTPEFVARHIIREAKSYLDNLAPPFFRALVDYAYDGSYSWHCPGHSGGVAFLKSPVGQ 184 Query: 177 FYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNR 236 +H ++GEN+ R+D+ LG LLDHTG SE+NAAR+F AD + V GTS SN+ Sbjct: 185 MFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNADHLFFVTNGTSTSNK 244 Query: 237 TIMQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETL 296 + +C+ D+V++DRNCHKS +I+TGA PV+++P+RN YGIIGPI E QP+T+ Sbjct: 245 IVWHSCVAAGDIVLVDRNCHKSNLHAIIMTGAIPVFLMPTRNHYGIIGPIPKSEFQPDTI 304 Query: 297 QKKISASP----LTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWY 352 +KKI A+P + + + +KP +T TYDG+ YN +E + LL D +HFDEAW Sbjct: 305 KKKILANPFAREMLEQRPNRKPRILTLTQSTYDGILYNVEEIKGLLDGEVDTLHFDEAWL 364 Query: 353 GYARFNPIYCDHYAM-RGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRG-AVNFS 410 +A F+ Y D +A+ G P + VF+T STHKLL +SQAS I V++ + ++ + Sbjct: 365 PHACFHDFYRDFHAIGEGRPRCEDS-LVFSTQSTHKLLAGISQASQILVQDPQNRQLDTA 423 Query: 411 RFNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFT 470 FN+AY+MH +TSP Y+I AS DVA +MM+ G SL +E + EA++FR+AM ++ +E+ Sbjct: 424 WFNEAYLMHTSTSPQYSIIASCDVAAAMMEQPGGQSLVEESLVEAMEFRRAMRKVDEEY- 482 Query: 471 DEGDWFFKPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWS 530 DW+F W D ++D DQ W +RP E WHGF + D ++ Sbjct: 483 -GRDWWFSVWGPDDLSDDG---------------ICDQTDWTLRPDERWHGFAGIEDGFN 526 Query: 531 MLDPIKVSILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRG 590 MLDPIK ++L PG+ DG E G+PAA+VT +L HG+V +T + +F++G+T+G Sbjct: 527 MLDPIKATVLTPGLDVDGSFEEMGIPAAIVTKYLTEHGVVVEKTGLYSFFIMFTIGITKG 586 Query: 591 KWGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGA 650 +W TLI+ L FK +D N PL +VMPE V YP Y +G+ DL ++ +++ Sbjct: 587 RWNTLISLLQQFKDDFDKNQPLWRVMPEFVAKYPQ-YDRVGLQDLCQRIHGLYTKHDVAR 645 Query: 651 RLNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGEN 710 Y + + P DA+ + + IE V ++ L GR+ A + PYPPGIP+L+ GE Sbjct: 646 LTTDIYLSDMEPAMRPADAFAKMAHREIERVPVDQLEGRVTAVLLTPYPPGIPLLIPGER 705 Query: 711 FGDENSPQVGYLRSLQSWDHHFPGFEHETEGTEIID----GVYHVMCVK 755 F N V YLR Q+++ PGFE + G ++ VY V CVK Sbjct: 706 F---NKTIVDYLRFAQAFNRELPGFETDVHGLVAVEVQDRKVYCVDCVK 751 Lambda K H 0.319 0.135 0.415 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: 1458 Number of extensions: 80 Number of successful extensions: 8 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: 756 Length of database: 752 Length adjustment: 40 Effective length of query: 716 Effective length of database: 712 Effective search space: 509792 Effective search space used: 509792 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 (21.8 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