Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate Pf1N1B4_4600 Lysine decarboxylase, inducible (EC 4.1.1.18)
Query= BRENDA::E8X9U7 (756 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4600 Length = 751 Score = 569 bits (1467), Expect = e-166 Identities = 306/765 (40%), Positives = 449/765 (58%), Gaps = 36/765 (4%) Query: 4 VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63 VLIV + + DT G+ V +A L Q+ +++ + +++G + S + + C++ + + Sbjct: 9 VLIVHRD-IKADTVAGDRVRGIARELEQEGFSIVSAVDYNEGRLVASTHHGLSCMLIAAE 67 Query: 64 MEQPDEHL--SVRQLIGKLHERQQNVPVFLLGDR---EKATASLDRDLLELVDEFAWILE 118 HL ++ +LI R ++P+F LG++ E A A +L +L ++ E Sbjct: 68 DASTHAHLLHNMAELIRLARVRAPDLPIFALGEQVTLENAPADAMAELNQLRG-ILYLFE 126 Query: 119 DTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFY 178 DT F+A + A +Y LLPP F AL++++ YSW PGH GGV + K+P G+ + Sbjct: 127 DTVPFLARQVARAARKYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYHKSPVGQAF 186 Query: 179 HDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTI 238 H ++GEN RSD+ + LGSLLDHTG E+E AAR FGAD ++ V+ GTS +N+ + Sbjct: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIV 246 Query: 239 MQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQK 298 + + +D+V++DRNCHKS+ +I+TGA P+Y+ P RN GIIGPI E E++Q Sbjct: 247 WHSMVARDDLVLVDRNCHKSVLHSIIMTGAIPLYLCPERNELGIIGPIPLSEFSRESIQA 306 Query: 299 KISASPLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFN 358 KI ASPLTK + K +VVTN TYDG+CYNA+ + L + + +HFDEAWY YA F+ Sbjct: 307 KIDASPLTKGRE-PKVKLAVVTNSTYDGLCYNAELIKQSLGNSVEVLHFDEAWYAYAAFH 365 Query: 359 PIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-VNFSRFNQAYM 417 + Y M G + P VF THSTHKLL A SQAS IHV++G ++ RFN+A+M Sbjct: 366 EFFAGRYGM-GTSRSEDSPLVFTTHSTHKLLAAFSQASMIHVQDGGARQLDRDRFNEAFM 424 Query: 418 MHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGDWFF 477 MH +TSP Y+I AS DVA +MM+G +G SL QE+ DEA+ FR+A+A L + + DW+F Sbjct: 425 MHISTSPQYSIIASLDVASAMMEGPAGRSLLQEMFDEALSFRRALANLRQHIAAD-DWWF 483 Query: 478 KPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKV 537 W + T D W+++P WHGF + D++ +LDPIKV Sbjct: 484 SIWQPPSAEGIEQVVTED---------------WLLQPDADWHGFGGVTDDYVLLDPIKV 528 Query: 538 SILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLIN 597 +++ PG+ G L A G+PAA+V+ +L G+V +T + + LFSMG+T+GKW TL+ Sbjct: 529 TLVMPGLTAGGALSARGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLT 588 Query: 598 TLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYS 657 L FK YDAN LA +P + Q Y MG+ DL D++ A R N L Y+ Sbjct: 589 ELLEFKRSYDANVSLATCLPCVAQHNVARYQGMGLRDLCDQLHACYRSNATAKHLKRMYT 648 Query: 658 TLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSP 717 LP + P DAY+ +V +E V+I+ L GRIAA ++PYPPGIP+++ GE F + Sbjct: 649 VLPEVAMKPADAYDQLVRGEVEAVSIDALDGRIAAVMLVPYPPGIPLIMPGERFTESTRS 708 Query: 718 QVGYLRSLQSWDHHFPGF-------EHETEGTEIIDGVYHVMCVK 755 + YL+ +++D FPGF +HE EG Y V C+K Sbjct: 709 IIDYLKFARTFDSSFPGFVADVHGLQHEDEGN---GRHYTVDCIK 750 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: 1375 Number of extensions: 65 Number of successful extensions: 6 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: 751 Length adjustment: 40 Effective length of query: 716 Effective length of database: 711 Effective search space: 509076 Effective search space used: 509076 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