Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate SMa0680 SMa0680 amino acid (ornithine, lysine, arginine) decarboxylase
Query= BRENDA::E8X9U7 (756 letters) >FitnessBrowser__Smeli:SMa0680 Length = 782 Score = 410 bits (1054), Expect = e-118 Identities = 230/663 (34%), Positives = 363/663 (54%), Gaps = 25/663 (3%) Query: 110 VDEFAWILEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGF 169 VD F ++ + T F A + ++++ Y + LLPP F LM Y ++ PGHQGG + Sbjct: 109 VDGFVYLGQQTPAFYAKQIISSLVNYGKTLLPPFFGGLMAYDGEANIAFDCPGHQGGQFY 168 Query: 170 TKTPAGRFYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVV 229 K+PAG+ + +Y+GE++FR+D+ LG LL H G E++KNAAR+FGADR++ ++ Sbjct: 169 RKSPAGQLFFNYFGESIFRADLCNADVDLGDLLIHEGPAAEAQKNAARIFGADRTYFILN 228 Query: 230 GTSGSNRTIMQACMTDNDVVVLDRNCHKSIEQG-LILTGAKPVYMVPSRNRYGIIGPIYP 288 GTS SN+ + A + D+V+ DRN HKS+ QG L+ GA PVY+ SRN +G+IG + Sbjct: 229 GTSTSNKVVTNAVLRAGDLVLFDRNNHKSLHQGALVQAGAIPVYLPTSRNSFGMIGAVDW 288 Query: 289 QEMQPETLQKKISASPLTKTKA---GQKP-SYSVVTNCTYDGVCYNAKEAQDLLAKTSDR 344 +L+++I PL + KA ++P + + TYDG YN ++ + + D Sbjct: 289 DAWDEASLRRQIERHPLVEDKARASAERPFRLACIQLATYDGTIYNVRKVLEQIGHLCDY 348 Query: 345 IHFDEAWYGYARFNPIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYI-----H 399 + +DEAW GY F+P++ DH MR + D P +F+T S HK SQAS I H Sbjct: 349 VLWDEAWIGYNAFHPLFEDHSPMRIDTLDAEMPGLFSTQSVHKQGAGFSQASQIHKRDEH 408 Query: 400 VREGRGAVNFSRFNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFR 459 +R+ R V RFN++ +MH +TSP Y + AS DV + +G +G L I+ ++ R Sbjct: 409 IRDQRRYVEHKRFNESLLMHVSTSPFYPLFASLDVNAKIHEGKAGEMLWDRCIELGIEAR 468 Query: 460 QAMARLYKEFTDEG-----DWFFKPWNKDVVTDPQTGKTYDFADA-----PAKLLATDQN 509 + + + + G WFF P+ DVVT + T D ++ P +++ +Q Sbjct: 469 KKLREFTRYYESSGAGPQEQWFFDPFVPDVVTISGSKHTEDVVESRWEALPTEVIKREQQ 528 Query: 510 CWVMRPGETWHGFKDLPDNWSMLDPIKVSILAPGMG-DDGELEASGVPAALVTAWLGRHG 568 CW RPG +WHG+ D ++M+DP K+++L PG+ GE G+PA +V +L Sbjct: 529 CWRFRPGASWHGYSGYSDGYAMVDPNKLTLLTPGIDRATGEYRDFGIPATMVANYLREQR 588 Query: 569 IVPTRTTDFQIMFLFSMGVTRGKWGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYA 628 IVP + I+FL + K TLI L FK+ +D + PLA+V+P + + YA Sbjct: 589 IVPEKCDLNSILFLLTPAEDESKLNTLIAKLVKFKNLWDRDAPLAEVLPTVFAANRERYA 648 Query: 629 NMGIHDLGDKMFAWLRENNPG--ARLNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENL 686 + + +M + R+ RL ++P +TP+ AY A+V N ++ VA++ Sbjct: 649 GYTLRQVCAEMHDFYRQAGVKELQRLCFRAESMPEPAMTPKAAYEALVANEVDYVALDEA 708 Query: 687 PGRIAANSVIPYPPGIPMLLSGENFGDENSPQVGYLRSLQSWDHHFPGFEHETEGT--EI 744 GRI+A + YPPGI +++ GE + + P Y + Q + FPGF +E +G E Sbjct: 709 FGRISATLALIYPPGIGVIVPGERWDERARPMHNYFLAFQESFNRFPGFNYEVQGVFQER 768 Query: 745 IDG 747 +DG Sbjct: 769 VDG 771 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: 1454 Number of extensions: 79 Number of successful extensions: 8 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: 782 Length adjustment: 41 Effective length of query: 715 Effective length of database: 741 Effective search space: 529815 Effective search space used: 529815 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