Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_109967963.1 DK846_RS05625 arginine decarboxylase
Query= BRENDA::P21169 (711 letters) >NCBI__GCF_003173355.1:WP_109967963.1 Length = 767 Score = 390 bits (1002), Expect = e-112 Identities = 246/687 (35%), Positives = 356/687 (51%), Gaps = 46/687 (6%) Query: 42 DSRSGILALLKRTGFHLPVFLYSEHAVELPAGVTAVINGNEQQWL------------ELE 89 +S + I+ ++R LP+FL +E A + P+G+T I +++ + Sbjct: 77 ESTTKIIHEIRRRNDELPIFLLAEPASQAPSGLTVEIIKEINEYVYAMDDTPDFLAGRIT 136 Query: 90 SAACQYEENLLPPFYDTLTQYVEMGNSTFACPGHQHGAFFKKHPAGRHFYDFFGENVFRA 149 +AA +Y E +L PF+ L ++ ++ PGH G F+K P GR F+ FFGE +FR+ Sbjct: 137 AAARRYREQMLSPFFSELIKFSRDFEYSWHTPGHAGGTAFRKTPVGRAFHTFFGEQLFRS 196 Query: 150 DMCNADVKLGDLLIHEGSAKDAQKFAAKVFHADKTYFVLNGTSAANKVVTNALLTRGDLV 209 D+ + +LG LL H G A+K+AAKVF ADKTYFV NGTS ANK+V +T GD+V Sbjct: 197 DLSISVDELGSLLDHSGPIGKAEKYAAKVFGADKTYFVTNGTSTANKIVFFGAVTEGDVV 256 Query: 210 LFDRNNHKSNHHGALIQAGATPVYLEASRNPFGFIGGIDAHCFNEEYLRQQIRDVAPEK- 268 L DRN HKS H AL + PVYL SRN +G IG I + + ++++ K Sbjct: 257 LVDRNCHKSAEH-ALTMTHSVPVYLIPSRNRYGIIGPIHPDQLTPDAISKKVQACPFTKY 315 Query: 269 ADLPRPYRLAIIQLGTYDGTVYNARQVIDTVGHLCDYILFDSAWVGYEQFIPMMADSSPL 328 AD P AII TYDG Y+A +V +G D I FD AW GY +F P+ D + Sbjct: 316 ADSDHPVH-AIITNSTYDGLCYHAARVEHLLGQTVDRIHFDEAWYGYARFNPLYRDRFAM 374 Query: 329 LLELNE-NDPGIFVTQSVHKQQAGFSQTSQIHKKDNHIRGQARFCPHKRLNNAFMLHAST 387 + N P +F TQS HK A SQ S +H ++ + H R N FM+H ST Sbjct: 375 RNGAKDSNGPTVFATQSTHKLLAALSQASMVHVRNGRVP-----IEHSRFNEGFMMHTST 429 Query: 388 SPFYPLFAALDVNAKIHEGESGRRLWAECVEIGIEARKAILARCK------------LFR 435 SP Y + A+LDV+AK+ +G SG+ L EC+E I R+ +AR F Sbjct: 430 SPLYTIIASLDVSAKMMDGPSGKILTDECIEEAIRFRRT-MARINREIGHRETPSDWWFG 488 Query: 436 PFIPPVV----DGK--LWQDYPTSVLASDRRFFSFEPGAKWHGFEGYAADQYFVDPCKLL 489 + P V GK + D P +L + + PG WHGFEG D +DP K+ Sbjct: 489 MWQPDAVTDPKSGKRISFTDAPLEILRDNPSCWVLHPGENWHGFEGLEDDYCMLDPIKVT 548 Query: 490 LTTPGIDAETGEYSDFGVPATILAHYLRENGIVPEKCDLNSILFLLTPAESHEKLAQLVA 549 + TPG+ A+ G FG+PA ++ +L GI+ EK SILFL + + K L+ Sbjct: 549 ILTPGV-ADDGRLEPFGIPAALVVKFLDTRGIINEKSGDYSILFLFSVGITKGKWGTLIT 607 Query: 550 MLAQFEQHIEDDSPLVEVLPSVYNKYPVRYRDYTLRQLCQEMHDLYVSFDVKDLQKAMFR 609 L +F++ ++++ L E+ P + YP RY TL +L +EMH D + L+ Sbjct: 608 ELFEFKRLYDENTLLEEIFPDLIESYPDRYSGMTLPELAEEMHAF--KRDHRMLETLSQA 665 Query: 610 QQSFPSVVMNPQDAHSAYIRGDVELVRIRDAEGRIAAEGALPYPPGVLCVVPGEVWG--- 666 P V+ DA+ +RG VE V + GR+ A G +PYPPG+ ++PGE G Sbjct: 666 FSLLPEPVITFADAYKRLVRGTVEQVPVEKMGGRVVATGVVPYPPGIPLLLPGERAGDQN 725 Query: 667 GAVQRYFLALEEGVNLLPGFSPELQGV 693 G + Y L++ + PGF+ + GV Sbjct: 726 GPILEYLKGLQDFDSRFPGFNHDTHGV 752 Lambda K H 0.322 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: 1314 Number of extensions: 66 Number of successful extensions: 9 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: 711 Length of database: 767 Length adjustment: 40 Effective length of query: 671 Effective length of database: 727 Effective search space: 487817 Effective search space used: 487817 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 24 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