Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate RR42_RS15940 RR42_RS15940 lysine decarboxylase
Query= SwissProt::Q9I2S7 (751 letters) >FitnessBrowser__Cup4G11:RR42_RS15940 Length = 754 Score = 748 bits (1930), Expect = 0.0 Identities = 377/760 (49%), Positives = 509/760 (66%), Gaps = 24/760 (3%) Query: 6 KFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVA 65 +FPV+I+ D +++ ++G +R +A +EQ+G ++ S + A + +V+ Sbjct: 4 RFPVIIIDEDFRSENISGSGIRALAQAIEQEGMEVMGLTSYGDLTSFAQQSSRASSFIVS 63 Query: 66 A---EGAGENQRLLQDVVELIRV----ARVRAPQLPIFALGEQVTIENAPAESMADLHQL 118 E E+ R +E +R R R LPIF GE T + P + + +LH Sbjct: 64 IDDDEFVSEDDRPEAAAIEKLRAFVNEVRRRNTDLPIFLYGETRTSRHIPNDILRELH-- 121 Query: 119 RGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYR 178 G +++FEDT F+AR + R AR YL L PPFF+AL+ + S+YSWH PGH GGVA+ Sbjct: 122 -GFIHMFEDTPEFVARHIIREARVYLDSLAPPFFKALIAYAQDSSYSWHCPGHSGGVAFL 180 Query: 179 KSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVING 238 KSPVGQ FHQFFGEN LR+D+ +V ELG LLDHTGP+A +E AAR F +DH +FV NG Sbjct: 181 KSPVGQVFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNSDHMYFVTNG 240 Query: 239 TSTANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSE 298 TST+NK+VWH+ V D+V+VDRNCHKSILH+I+MTGAIP++L P RN GIIGPIP SE Sbjct: 241 TSTSNKMVWHANVAPGDIVVVDRNCHKSILHAIMMTGAIPVFLMPTRNHYGIIGPIPKSE 300 Query: 299 FSKQSIAAKIAASPLA-RGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEA 357 F ++I KIAA P A + + K ++ +T TYDG+ YNAE IK+ L ++ LHFDEA Sbjct: 301 FDPETIRRKIAAHPFASQAKNQKPRILTITQGTYDGVLYNAEQIKEMLATEIDTLHFDEA 360 Query: 358 WYAYAAFHEFYDGRYGMGTSR-SEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDV 416 W +AAFH+FY + +G R + LVFAT STHK+LA SQAS I VQD TRKLD Sbjct: 361 WLPHAAFHDFYHNMHAIGRDRPRSKDALVFATQSTHKLLAGLSQASQILVQDSDTRKLDR 420 Query: 417 ARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNL 476 RFNEA++MH STSPQY IIAS DVA+AMME P G +L++E+ EA+ FRRA+ V + Sbjct: 421 YRFNEAYLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESIQEAMDFRRAMRKVEGDY 480 Query: 477 D---RNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTP 533 D DWWF VW PE + D +W+L+ + WHGFGD+A+ + LLDPIK T+ TP Sbjct: 481 DAGNNGDWWFKVWGPEALAEDDIGDREEWMLKANERWHGFGDLADGFNLLDPIKATIITP 540 Query: 534 GLSAGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEF 593 GL G+ S++GIPAAIV+++L E G+++EKTGLYSF ++F++GITKG+W++LVTEL +F Sbjct: 541 GLDVDGEFSDRGIPAAIVTKYLAEHGIIIEKTGLYSFFIMFTIGITKGRWNSLVTELQQF 600 Query: 594 KRCYDANLPLLDVLPSVAQAGGK--RYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLP 651 K YD N PL VLP GK +Y +GLRDL DA+H+ Y+ N A+ MY Sbjct: 601 KDDYDQNQPLWRVLPEFV---GKHPQYEKLGLRDLCDAIHSVYKANDVARVTTEMYLSDM 657 Query: 652 EVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILD 711 E AM+PS+A+ + E+E V + LEGR+ A++L PYPPGIPL++PGERF R I+ Sbjct: 658 EPAMKPSDAWAMMAHREIERVAVDELEGRVTAILLTPYPPGIPLLIPGERF---NRIIVQ 714 Query: 712 YLEFARTFERAFPGFDSDVHGLQHQD-GPSGRCYTVECIK 750 YL+FAR F + FPGF++D+HGL ++ G+ Y V+C+K Sbjct: 715 YLKFAREFNKLFPGFETDIHGLVEEEVEGGGKAYFVDCVK 754 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: 1384 Number of extensions: 49 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: 751 Length of database: 754 Length adjustment: 40 Effective length of query: 711 Effective length of database: 714 Effective search space: 507654 Effective search space used: 507654 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 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