Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate SMa0682 SMa0682 decarboxylase (lysine, ornithine, arginine)
Query= SwissProt::Q9I2S7 (751 letters) >FitnessBrowser__Smeli:SMa0682 Length = 756 Score = 863 bits (2231), Expect = 0.0 Identities = 429/748 (57%), Positives = 544/748 (72%), Gaps = 8/748 (1%) Query: 7 FPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAA 66 FP+ ++ D + + AG +R +A +E++G+ +++ + + R + + + +C L++ Sbjct: 7 FPIAVIDEDYEGKSAAGRGMRSLAEAIEKEGYRVVAGLTYEDARRLVNVFNTESCWLISV 66 Query: 67 EGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLFE 126 +G + + + EL+ R R LPIF G+ T E PA L + LFE Sbjct: 67 DGTESSTTRWEILAELLAAKRSRNNLLPIFLFGDDTTAEMVPAPV---LRHANAFMRLFE 123 Query: 127 DTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAF 186 D+ F+AR + RAA+NYL L PP F+AL+E+T YSWHTPGHGGGVA+RKSPVGQ F Sbjct: 124 DSPEFMARAIVRAAQNYLERLPPPMFKALMEYTLHGAYSWHTPGHGGGVAFRKSPVGQLF 183 Query: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIV 246 + FFGENTLRSD+SVSV +GSLLDH GP+ E E AAR FGAD T FV+ GTSTANKIV Sbjct: 184 YTFFGENTLRSDISVSVGSVGSLLDHVGPIGEGERNAARIFGADETLFVVGGTSTANKIV 243 Query: 247 WHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAA 306 W MV R DLVL DRNCHKSILHS+IMTGA P+YLTP RN LGIIGPI +F+ ++IA Sbjct: 244 WQGMVTRNDLVLCDRNCHKSILHSLIMTGATPIYLTPSRNGLGIIGPIAKEQFTPEAIAH 303 Query: 307 KIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHE 366 KI ASP A KV+L VVTNSTYDGLCYN + IK LGD+VEVLHFDEAW+AYA FHE Sbjct: 304 KIVASPFASETNGKVRLMVVTNSTYDGLCYNVDGIKSALGDAVEVLHFDEAWFAYANFHE 363 Query: 367 FYDGRYGMGT---SRSEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFNEAF 423 FYDG + + + +RS+E + FAT STHK+LAAFSQASM+HVQ ++LD+ RFNEAF Sbjct: 364 FYDGYHAISSTKPARSQEA-ITFATQSTHKLLAAFSQASMLHVQHAVAKQLDITRFNEAF 422 Query: 424 MMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRNDWWF 483 MMH STSPQYGIIAS DVA+AMME PAGR+L+QET DEA+SFRRA+ VR + ++ WWF Sbjct: 423 MMHTSTSPQYGIIASCDVAAAMMEQPAGRALVQETIDEAMSFRRAVNAVRTQM-QDSWWF 481 Query: 484 GVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGKLSE 543 VW+P + T DW+L+P WHGF D+AE++V++DPIKVT+ +PGL+AGG + E Sbjct: 482 EVWEPPIADRAPSDATSDWLLKPGDAWHGFEDLAENHVMVDPIKVTILSPGLNAGGAMLE 541 Query: 544 QGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDANLPL 603 GIPAA+V++FL R + +EKTGLYSFLVLFSMGIT+GKWSTL+TELL FK YDAN PL Sbjct: 542 HGIPAAVVTKFLSSRRIEIEKTGLYSFLVLFSMGITRGKWSTLITELLNFKDLYDANAPL 601 Query: 604 LDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEAYDK 663 LP++A A Y +GLRDL + +H YR + A + MYTVLPE+A+RP++AY++ Sbjct: 602 SRALPALAAAHPDVYRAMGLRDLCEKIHDVYRSDGVPNAQREMYTVLPEMALRPADAYNR 661 Query: 664 LVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFERAF 723 LV+G VE+V I L GR AVM+VPYPPGIPLIMPGER T ATRSI DYL +AR+F+R F Sbjct: 662 LVKGCVESVDIDELIGRTLAVMIVPYPPGIPLIMPGERITAATRSIQDYLVYARSFDRKF 721 Query: 724 PGFDSDVHGLQHQDGPSGRCYTVECIKE 751 PGF++D+HGL+ PSGR Y V+CI E Sbjct: 722 PGFETDIHGLRFVANPSGRRYLVDCIVE 749 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: 1454 Number of extensions: 47 Number of successful extensions: 4 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: 756 Length adjustment: 40 Effective length of query: 711 Effective length of database: 716 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