Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate SMa0680 SMa0680 amino acid (ornithine, lysine, arginine) decarboxylase
Query= BRENDA::A4Q8H0 (720 letters) >FitnessBrowser__Smeli:SMa0680 Length = 782 Score = 704 bits (1818), Expect = 0.0 Identities = 376/743 (50%), Positives = 482/743 (64%), Gaps = 41/743 (5%) Query: 16 FETE-REIVDVHQSDFNDVAAIVLSVE----DVAKGMVTHLEEIGLNIPLFVAVCCEEEL 70 FE E R + S+ V A + +VE + A+ V + +IG PL+ Sbjct: 39 FEVELRGSYNADVSEDASVGAYIGTVEGGRLEDARKFVRAVRDIGFRTPLWALADSHGIA 98 Query: 71 DNAVLPALHGV--FELCGKNTQ-FYGKQLEAAAVKYEKDLLPPFFNTLTQYVEMGNATFA 127 D A + V F G+ T FY KQ+ ++ V Y K LLPPFF L Y N F Sbjct: 99 DIAAIKMAGEVDGFVYLGQQTPAFYAKQIISSLVNYGKTLLPPFFGGLMAYDGEANIAFD 158 Query: 128 CPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCNADVKLGDLLIHEGLPCAAQQHAAKVF 187 CPGHQGG+F+RK PAG+ FF+++GE++FR+D+CNADV LGDLLIHEG AQ++AA++F Sbjct: 159 CPGHQGGQFYRKSPAGQLFFNYFGESIFRADLCNADVDLGDLLIHEGPAAEAQKNAARIF 218 Query: 188 NADKTYFVLNGTSASNKVATNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLETARN 247 AD+TYF+LNGTS SNKV TNA+L GDLVLFDRNNHKS H GAL+QAGA PVYL T+RN Sbjct: 219 GADRTYFILNGTSTSNKVVTNAVLRAGDLVLFDRNNHKSLHQGALVQAGAIPVYLPTSRN 278 Query: 248 PFGFIGGIDAHCFDERYLRQQIRE----VAPERANEARPFRLAIIQLGTYDGTIYNARQV 303 FG IG +D +DE LR+QI RA+ RPFRLA IQL TYDGTIYN R+V Sbjct: 279 SFGMIGAVDWDAWDEASLRRQIERHPLVEDKARASAERPFRLACIQLATYDGTIYNVRKV 338 Query: 304 VDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLE-LNENDPGIIVTQSVHKQQAGFSQ 362 +++IGHLCDY+L+D AW+GY F P+ +D SP+ ++ L+ PG+ TQSVHKQ AGFSQ Sbjct: 339 LEQIGHLCDYVLWDEAWIGYNAFHPLFEDHSPMRIDTLDAEMPGLFSTQSVHKQGAGFSQ 398 Query: 363 TSQIHKKDKHIKGQSRYCNHKRFNNAFMLHASTSPFYPLFAALDVNAKMHEGKSGQRLWK 422 SQIHK+D+HI+ Q RY HKRFN + ++H STSPFYPLFA+LDVNAK+HEGK+G+ LW Sbjct: 399 ASQIHKRDEHIRDQRRYVEHKRFNESLLMHVSTSPFYPLFASLDVNAKIHEGKAGEMLWD 458 Query: 423 ECVRVGIEARKMLLETCQ-------------LIKPFVPD--QIDGKP---------WQSY 458 C+ +GIEARK L E + PFVPD I G W++ Sbjct: 459 RCIELGIEARKKLREFTRYYESSGAGPQEQWFFDPFVPDVVTISGSKHTEDVVESRWEAL 518 Query: 459 DTETMANDLRFFNFVPGEKWHAFEGYAESQYFVDPCKLLLTTPGIDTASGNYSDFGIPAT 518 TE + + + + F PG WH + GY++ VDP KL L TPGID A+G Y DFGIPAT Sbjct: 519 PTEVIKREQQCWRFRPGASWHGYSGYSDGYAMVDPNKLTLLTPGIDRATGEYRDFGIPAT 578 Query: 519 ILANYLRENGIVPEKCDLNSILFLLTPAEDIAKMQHLVALIARFEKHIEQDSLLSEVLPA 578 ++ANYLRE IVPEKCDLNSILFLLTPAED +K+ L+A + +F+ ++D+ L+EVLP Sbjct: 579 MVANYLREQRIVPEKCDLNSILFLLTPAEDESKLNTLIAKLVKFKNLWDRDAPLAEVLPT 638 Query: 579 VYKSNEQRYKNYTLRQLCQEMHDLYVSYDVKELQKEMFRKNYFPRIAMNPQDANTEFVRG 638 V+ +N +RY YTLRQ+C EMHD Y VKELQ+ FR P AM P+ A V Sbjct: 639 VFAANRERYAGYTLRQVCAEMHDFYRQAGVKELQRLCFRAESMPEPAMTPKAAYEALVAN 698 Query: 639 NIELVSLAKAEGRIAAEGALPYPPGVLCVVPGEIWGGAAQ---RYFLALEEGINLLPGFA 695 ++ V+L +A GRI+A AL YPPG+ +VPGE W A+ YFLA +E N PGF Sbjct: 699 EVDYVALDEAFGRISATLALIYPPGIGVIVPGERWDERARPMHNYFLAFQESFNRFPGFN 758 Query: 696 PELQGVYIQQDEDGWNRAYGYVM 718 E+QGV+ Q+ DG + Y Y + Sbjct: 759 YEVQGVF-QERVDGQIKFYTYAV 780 Lambda K H 0.321 0.138 0.420 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: 1554 Number of extensions: 92 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: 720 Length of database: 782 Length adjustment: 40 Effective length of query: 680 Effective length of database: 742 Effective search space: 504560 Effective search space used: 504560 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 (21.9 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