Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate WP_046156677.1 VL52_RS08800 arginine/lysine/ornithine decarboxylase
Query= SwissProt::Q9I2S7 (751 letters) >NCBI__GCF_000971335.1:WP_046156677.1 Length = 752 Score = 717 bits (1852), Expect = 0.0 Identities = 367/758 (48%), Positives = 491/758 (64%), Gaps = 23/758 (3%) Query: 7 FPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAA 66 FP++I+ D +++ +G +R +A +E +G S++ S + A A +++ Sbjct: 5 FPIVIIDEDFRSENTSGSGIRELAAAMEAEGMSVIGYTSYGDLTSFAQQQSRAAGFILSI 64 Query: 67 EG-----AGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGI 121 + Q L ++ + R R P +P++ GE T + P + + +LH G Sbjct: 65 DDEEFQTVDSAQESLGNLYGFVAEIRRRNPDIPVYLYGETRTARHIPNDILRELH---GF 121 Query: 122 LYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSP 181 +++ EDT F+AR + R A++YL L PPFFRALV++ +YSWH PGH GGVA+ KSP Sbjct: 122 IHMHEDTPEFVARHIIREAKSYLDNLAPPFFRALVDYAYDGSYSWHCPGHSGGVAFLKSP 181 Query: 182 VGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTST 241 VGQ FHQFFGEN LR+D+ +V ELG LLDHTGP+A +E AAR F ADH FFV NGTST Sbjct: 182 VGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNADHLFFVTNGTST 241 Query: 242 ANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSK 301 +NKIVWHS V D+VLVDRNCHKS LH+IIMTGAIP++L P RN GIIGPIP SEF Sbjct: 242 SNKIVWHSCVAAGDIVLVDRNCHKSNLHAIIMTGAIPVFLMPTRNHYGIIGPIPKSEFQP 301 Query: 302 QSIAAKIAASPLAR-------GREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHF 354 +I KI A+P AR R+P++ +T STYDG+ YN E IK L V+ LHF Sbjct: 302 DTIKKKILANPFAREMLEQRPNRKPRI--LTLTQSTYDGILYNVEEIKGLLDGEVDTLHF 359 Query: 355 DEAWYAYAAFHEFYDGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQDGGTRK 413 DEAW +A FH+FY + +G R E LVF+T STHK+LA SQAS I VQD R+ Sbjct: 360 DEAWLPHACFHDFYRDFHAIGEGRPRCEDSLVFSTQSTHKLLAGISQASQILVQDPQNRQ 419 Query: 414 LDVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVR 473 LD A FNEA++MH STSPQY IIAS DVA+AMME P G+SL++E+ EA+ FRRA+ V Sbjct: 420 LDTAWFNEAYLMHTSTSPQYSIIASCDVAAAMMEQPGGQSLVEESLVEAMEFRRAMRKVD 479 Query: 474 QNLDRNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTP 533 + R DWWF VW P+ + DW L P WHGF I + + +LDPIK T+ TP Sbjct: 480 EEYGR-DWWFSVWGPDDLSDDGICDQTDWTLRPDERWHGFAGIEDGFNMLDPIKATVLTP 538 Query: 534 GLSAGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEF 593 GL G E GIPAAIV+++L E G+VVEKTGLYSF ++F++GITKG+W+TL++ L +F Sbjct: 539 GLDVDGSFEEMGIPAAIVTKYLTEHGVVVEKTGLYSFFIMFTIGITKGRWNTLISLLQQF 598 Query: 594 KRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEV 653 K +D N PL V+P A +Y+ VGL+DL +H Y + A+ +Y E Sbjct: 599 KDDFDKNQPLWRVMPEFV-AKYPQYDRVGLQDLCQRIHGLYTKHDVARLTTDIYLSDMEP 657 Query: 654 AMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYL 713 AMRP++A+ K+ E+E VP+ +LEGR+ AV+L PYPPGIPL++PGERF ++I+DYL Sbjct: 658 AMRPADAFAKMAHREIERVPVDQLEGRVTAVLLTPYPPGIPLLIPGERF---NKTIVDYL 714 Query: 714 EFARTFERAFPGFDSDVHGLQHQDGPSGRCYTVECIKE 751 FA+ F R PGF++DVHGL + + Y V+C+K+ Sbjct: 715 RFAQAFNRELPGFETDVHGLVAVEVQDRKVYCVDCVKQ 752 Lambda K H 0.320 0.136 0.407 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: 1397 Number of extensions: 46 Number of successful extensions: 7 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: 751 Length of database: 752 Length adjustment: 40 Effective length of query: 711 Effective length of database: 712 Effective search space: 506232 Effective search space used: 506232 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