Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate GFF2032 Psest_2075 Arginine/lysine/ornithine decarboxylases
Query= BRENDA::E8X9U7 (756 letters) >FitnessBrowser__psRCH2:GFF2032 Length = 749 Score = 572 bits (1475), Expect = e-167 Identities = 310/762 (40%), Positives = 447/762 (58%), Gaps = 32/762 (4%) Query: 4 VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63 +LIV + + DT G V +A L + ++ + S ++G + S + + C++ + + Sbjct: 9 ILIVHRD-IKADTVAGERVRGIASELERDGFNILPTASSNEGRIVASTHHGLACILVAAE 67 Query: 64 MEQPDEHL--SVRQLIGKLHERQQNVPVFLLGDR---EKATASLDRDLLELVDEFAWILE 118 ++ L V +LI R +P+F LG++ E A A DL EL ++ E Sbjct: 68 GAGDNQRLLHDVVELIRVARRRAPRLPIFALGEQVTIENAPAEAMADLNELRG-LLYLYE 126 Query: 119 DTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFY 178 DT F+A + A Y LLPP F+AL++++ YSW PGH GGV + K+P G+ + Sbjct: 127 DTVPFLARQVARAARSYLDDLLPPFFSALVRHTGESNYSWHTPGHGGGVAYRKSPVGQAF 186 Query: 179 HDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTI 238 H ++GEN RSD+ + LGSLLDHTG +E AAR FGAD ++ V+ GTS +N+ + Sbjct: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPVAAAEARAARNFGADHTFFVINGTSTANKIV 246 Query: 239 MQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQK 298 + + +D+V++DRNCHKSI +I+TGA P+YM P+RN GIIGPI +E E++Q Sbjct: 247 WHSMVARDDLVLVDRNCHKSILHAIIMTGAIPLYMSPTRNELGIIGPIPLEEFTRESIQA 306 Query: 299 KISASPLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFN 358 KI+A+PL + + K +VVTN TYDG+CYNA + LA + +HFDEAWY YA F+ Sbjct: 307 KIAANPLARGRP-PKVKLAVVTNSTYDGLCYNANLIKRTLADNVEVLHFDEAWYAYAAFH 365 Query: 359 PIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-VNFSRFNQAYM 417 Y Y M GP VF THSTHKLL A SQAS IHV + + ++ RFN+A+M Sbjct: 366 EFYDGRYGMDTR---EQGPLVFTTHSTHKLLAAFSQASMIHVLDSQTRQLDRDRFNEAFM 422 Query: 418 MHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGDWFF 477 MH +TSP Y I AS DVA +MM+G +G SL QE DEA+ FR+A+A L ++ D DW+F Sbjct: 423 MHISTSPQYGILASLDVASAMMEGPAGRSLIQETFDEALSFRRALANL-RQHIDADDWWF 481 Query: 478 KPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKV 537 W +V D L+ D W++ P WHGF ++ D++ +LDPIKV Sbjct: 482 SIWQPPLV------------DGAEALVTPD---WLLEPTADWHGFGEIADDYVLLDPIKV 526 Query: 538 SILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLIN 597 +++ PG+ G L SG+PAA+V+ +L G+V +T + ++ LFSMG+T+GKW TL+ Sbjct: 527 TLVTPGLTASGALGKSGIPAAVVSKFLWERGLVVEKTGLYSMLVLFSMGITKGKWSTLLT 586 Query: 598 TLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYS 657 L FK HYDAN PL + +P + + TYA MG+ DL D + A EN + Y+ Sbjct: 587 ELLEFKRHYDANIPLVEALPSIARKGAATYAGMGLRDLCDALHACYCENATARAMRRMYT 646 Query: 658 TLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSP 717 LP +TP AY+ +V +E V IE L GRIAA ++PYPPGIP+++ GE F E Sbjct: 647 ALPEPAMTPAQAYDKLVRGEVEAVPIEALEGRIAAVMLVPYPPGIPLIMPGERFTGETRS 706 Query: 718 QVGYLRSLQSWDHHFPGFEHETEGTEIIDGV----YHVMCVK 755 + YLR + + FPGF+ + G + GV Y V C++ Sbjct: 707 ILDYLRFARDFAERFPGFDADVHGLQHEVGVGGSSYTVDCIR 748 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: 1366 Number of extensions: 62 Number of successful extensions: 5 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: 749 Length adjustment: 40 Effective length of query: 716 Effective length of database: 709 Effective search space: 507644 Effective search space used: 507644 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