Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BWI76_RS07195 BWI76_RS07195 lysine decarboxylase CadA
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__Koxy:BWI76_RS07195 Length = 715 Score = 335 bits (860), Expect = 4e-96 Identities = 211/620 (34%), Positives = 321/620 (51%), Gaps = 32/620 (5%) Query: 114 EIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENI 173 +I+ +Y D +LPP KAL YV G F PGH GG F+KSP G FY+F+G N Sbjct: 116 KIKQNTDEYIDTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGSNT 175 Query: 174 FRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPG 233 +SDI + +LG LL H GP +AE++ ARVFNA+++Y V NGT+T+N I + G Sbjct: 176 MKSDISISVSELGSLLDHSGPHKEAEEYIARVFNAERSYMVTNGTSTANKIVGMYSAPAG 235 Query: 234 DLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDP 293 VL DRN HKS+ + ++ + P+Y +R++YG +GGI +F +I +++ Sbjct: 236 STVLIDRNCHKSLTH-LMMMSDITPIYFRPTRNAYGILGGIPQSEFQHATIAKRV----K 290 Query: 294 EKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSS 353 E A P AVI TYDG +YN + + + I FDSAWV Y F P+ + Sbjct: 291 ETPNATWPVH-AVITNSTYDGLLYNTDYIKKTLD--VKSIHFDSAWVPYTNFSPIYEGKC 347 Query: 354 PLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSS 413 + + I TQSTHK A FSQAS I H+KG +N + FN AYM ++ Sbjct: 348 G-MSGGRVEGKVIYETQSTHKLLAAFSQASMI-----HVKGD---VNEETFNEAYMMHTT 398 Query: 414 TSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKP 473 TSP Y + A+ + A M +G AGK+L ++ S+ RK + + + V Sbjct: 399 TSPHYGVVASTETAAAMMKGNAGKRLIDGSIERSIKFRKEIKRLKGESDGWFFDV----- 453 Query: 474 WQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFG 533 WQ + + + W + WHGF + ++DP K L TPG+ + G +DFG Sbjct: 454 WQ----PEHIDGAECWPLRSDSAWHGFKNIDNEHMYLDPIKVTLLTPGMK-KDGTMDDFG 508 Query: 534 IPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDE 593 IPA I+A YL EHGI+ EK ++LFL + + K +L+ + F+ + + Sbjct: 509 IPASIVAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAFDLNLRVKN 568 Query: 594 VLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVE 653 +LP LY E + YE +++L Q +H +++N + F + P +TPY A + Sbjct: 569 MLPSLYREDPEFYENMRVQELAQNIHKLIEHHNLPDLMFRAF--EVLPTMMITPYAAFQK 626 Query: 654 LLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQ---KYFLILEESINRF 710 L + V L ++ G LPYPPG+ ++PGE T+ ++ ++ +L E + Sbjct: 627 ELHGQTEEVYLEEMVGRVNANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHY 686 Query: 711 PGFAPEIQGVYFEKENGKSV 730 PGF +I G Y + + +V Sbjct: 687 PGFETDIHGAYRQADGRYTV 706 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: 1298 Number of extensions: 73 Number of successful extensions: 10 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: 715 Length adjustment: 40 Effective length of query: 705 Effective length of database: 675 Effective search space: 475875 Effective search space used: 475875 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