Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate Dsui_1245 Dsui_1245 arginine/lysine/ornithine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__PS:Dsui_1245 Length = 746 Score = 402 bits (1034), Expect = e-116 Identities = 238/683 (34%), Positives = 370/683 (54%), Gaps = 30/683 (4%) Query: 63 KAIINKADETKFNIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLYDREIEAAAK 120 +A +++ IPIF+ T S + + + ++ I + + + R + AK Sbjct: 83 RAFVSEIRLRNSEIPIFLHGETRTSRHIPNDVLRELHGFIHMYEDTPEFIA-RNVVREAK 141 Query: 121 KYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICN 180 Y + + PPFF+AL Y G+ + CPGH GG F KSP G+ F+ F+GEN+ R+D+CN Sbjct: 142 AYLESLPPPFFRALTHYASDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCN 201 Query: 181 ADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDR 240 A +LG LL H GP +E++AAR+FN D YFV NGT+TSN I + VAPGD+V+ DR Sbjct: 202 AVEELGQLLDHTGPVAASERNAARIFNCDHLYFVTNGTSTSNKIVWHSTVAPGDIVVVDR 261 Query: 241 NNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAKR 300 N HKS+ + A++ G PV+L +R+++G IG I +F ++I++KIA K + Sbjct: 262 NCHKSILH-AIMMTGAIPVFLMPTRNNFGIIGPIPKSEFAWENIQKKIAANPFATDKNAK 320 Query: 301 PFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLG 360 P R+ I TYDG +YN + + E + D + FD AW+ + F D +G Sbjct: 321 P-RVLTITQSTYDGILYNVEAIKEELDGKIDTLHFDEAWLPHAAFHDFYGDYHA----IG 375 Query: 361 PDDPG-----ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTS 415 D P + TQSTHK AG SQASQI +D+ + +++ FN AY+ +STS Sbjct: 376 ADRPRCKESMVFSTQSTHKLLAGLSQASQILVQDA----ENSHLDRDVFNEAYLMHTSTS 431 Query: 416 PFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKPWQ 475 P Y + A+ D+ A M E G L +++ +++ R+ + K + K W Sbjct: 432 PQYAIIASCDVAAAMMEEPGGTALVEESIAEALDFRRAMRK----VDEEWGSGWWFKVWG 487 Query: 476 DAD-TEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGI 534 D +E+ + + D W + G +WHGF AD +DP K + TPG+DV+ GE+ + GI Sbjct: 488 PDDLSEEGIEERDAWMLKPGDRWHGFGNLADGFNMLDPIKATIITPGLDVD-GEFAERGI 546 Query: 535 PAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEV 594 PA I+ YL EHG+I EK L S + T T+ + +++VT++ +F+ + PL +V Sbjct: 547 PAAIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNSMVTELQQFKDDYDKNQPLWKV 606 Query: 595 LPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVEL 654 LP ++H RYE ++ LC+E+H Y++N+ EM+L P AM P A ++ Sbjct: 607 LPAFVAKH-PRYERVGLRDLCREIHAVYRSNDVARLTTEMYLSDMVP--AMKPADAFAKM 663 Query: 655 LKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFLILEESINRFPGFA 714 VP+ ++EG PYPPGI ++PGE++ + +Y + +FPGF Sbjct: 664 AHREIDRVPIDELEGRVTSVLLTPYPPGIPLLIPGERFNRTIMQYLQFARDFNEKFPGFE 723 Query: 715 PEIQGVYFEKENGKSVAYGYVYD 737 +I G+ E+ +GK GY D Sbjct: 724 TDIHGLVKEERDGK---VGYYVD 743 Lambda K H 0.318 0.136 0.405 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: 1291 Number of extensions: 52 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: 745 Length of database: 746 Length adjustment: 40 Effective length of query: 705 Effective length of database: 706 Effective search space: 497730 Effective search space used: 497730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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