Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate GFF2401 PS417_12240 lysine decarboxylase
Query= BRENDA::P28629 (755 letters) >FitnessBrowser__WCS417:GFF2401 Length = 751 Score = 574 bits (1480), Expect = e-168 Identities = 307/762 (40%), Positives = 451/762 (59%), Gaps = 30/762 (3%) Query: 3 VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQ 62 VLIV + + DT G+ V +A L Q+ ++ + + +G + S++ + C++ + + Sbjct: 9 VLIVHRD-IKADTVAGDRVRGIARELEQEGFSIFSAVDYAEGRLVASTHHGLACMLIAAE 67 Query: 63 MEHPDEH--QNVRQLIGKLHERQQNVPVFLLGDR---EKALAAMDRDLLELVDEFAWILE 117 + H QN+ +LI R N+P+F LG++ E A A +L +L ++ E Sbjct: 68 GAGENTHLLQNMVELIRLARLRAPNLPIFALGEQVTLENAPADAMSELNQLRG-ILYLFE 126 Query: 118 DTADFIAGRAVAAMTRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFY 177 DT F+A + A Y LLPP F AL++++ YSW PGH GGV + K+P G+ + Sbjct: 127 DTVPFLARQVARAARTYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYRKSPVGQAF 186 Query: 178 HDYYGENLFRTDMGIERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTI 237 H ++GEN R+D+ + LGSLLDHTG E+E AAR FGAD ++ V+ GTS +N+ + Sbjct: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIV 246 Query: 238 MQACMTDNDVVVVDRNCHKSIEQGLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQK 297 + + +D+V+VDRNCHKS+ +++TGA P+Y+ P RN GIIGPI E PE+++ Sbjct: 247 WHSMVGRDDLVLVDRNCHKSVLHSIIMTGAIPLYLCPERNELGIIGPIPLSEFSPESIRA 306 Query: 298 KISESPLTKDKAGQKPSYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFN 357 KI SPLT+ + K VVTN TYDG+CYNA+ + L + + LHFDEAWY YA F+ Sbjct: 307 KIDASPLTRGRP-PKVKLAVVTNSTYDGLCYNAELIKQQLGNSVEVLHFDEAWYAYAAFH 365 Query: 358 PIYADHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-INFSRFNQAYM 416 +A Y M G + P VF THSTHKLL A SQAS IHV++G ++ RFN+A+M Sbjct: 366 EFFAGRYGM-GTSRTPDSPLVFTTHSTHKLLAAFSQASMIHVQDGGARQLDRDRFNEAFM 424 Query: 417 MHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFF 476 MH +TSP Y+I AS DVA +MM+G +G SL QE+ DEA+ FR+A+A L ++ A+ W+F Sbjct: 425 MHISTSPQYSIIASLDVASAMMEGPAGRSLLQEMFDEALSFRRALANL-RQHIAEEDWWF 483 Query: 477 KPWNKEVVTDPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKV 536 W V T D W++HP + WHGF D+ +++ +LDPIKV Sbjct: 484 SIWQPPSVAGIDRVVTAD---------------WLLHPQDDWHGFGDVAEDYVLLDPIKV 528 Query: 537 SILAPGMGEDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVN 596 +++ PG+ G L + G+PAA+V+ +L G+V +T + + LFSMG+T+GKW TL+ Sbjct: 529 TLVMPGLTAGGALSDCGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLT 588 Query: 597 TLCSFKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYS 656 L FKR YDAN LA +P + Q P Y +G+ DL D + + + N L Y+ Sbjct: 589 ELLEFKRSYDANVSLASCLPSVFAQGPTRYQGLGLRDLCDQLHSCYRSNATAKHLKRMYT 648 Query: 657 GLPVAEVTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSP 716 LP + P +AY+ +V VE VSI+ LPGRIAA ++PYPPGIP+++ GE F + Sbjct: 649 VLPEIAMKPADAYDQLVRGEVEAVSIDALPGRIAAVMLVPYPPGIPLIMPGERFTESTRS 708 Query: 717 QVSYLRSLQSWDHHFPGFEHETEGTEIIDG----IYHVMCVK 754 + YL +++D FPGF + G + D Y V C+K Sbjct: 709 IIDYLAFARTFDSSFPGFVADVHGLQHEDDGSGRCYTVDCIK 750 Lambda K H 0.319 0.135 0.414 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: 1413 Number of extensions: 68 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: 755 Length of database: 751 Length adjustment: 40 Effective length of query: 715 Effective length of database: 711 Effective search space: 508365 Effective search space used: 508365 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 (21.7 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