Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BWI76_RS05300 BWI76_RS05300 lysine decarboxylase LdcC
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__Koxy:BWI76_RS05300 Length = 712 Score = 331 bits (849), Expect = 7e-95 Identities = 221/689 (32%), Positives = 350/689 (50%), Gaps = 47/689 (6%) Query: 45 ADNSDFVD----VAAVVVMDDEKAIINKADETKFN--IPIFIITDDSSKVDGETMSKIFH 98 AD F++ + V+ DE ++ +D + N +P++ + S +D S+ Sbjct: 40 ADLLQFIEHNPRICGVIFDWDEYSVDLCSDINRLNEYLPLYAFINAHSTMD--VSSQDLR 97 Query: 99 IIDWHNNYDRRLYDR---EIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQY 155 + W Y L + I ++Y D + PPF KAL YV+ G F PGH GG Sbjct: 98 MTLWFFEYALGLAEEIATRIGQYTREYLDNITPPFTKALFNYVQEGKYTFCTPGHMGGSA 157 Query: 156 FRKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVM 215 ++KSP G FY+F+G N ++D+ + +LG LL H GP ++AE++ AR F A+++Y V Sbjct: 158 YQKSPVGCLFYDFFGGNTLKADVSISVTELGSLLDHSGPHLEAEEYIARAFGAEQSYMVT 217 Query: 216 NGTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIY 275 NGT+TSN I + G +L DRN HKS+ + L+ + P++L+ +R++ G +GGI Sbjct: 218 NGTSTSNKIVGMYSAPAGSTLLIDRNCHKSLAH-LLMMSDVVPLWLKPTRNALGILGGIP 276 Query: 276 SKDFDEKSIREKIAKVDPEKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILF 335 ++F SI++K+ A P AVI TYDG +YN + E + I F Sbjct: 277 KREFTRDSIQQKVNTT----GGAGWPVH-AVITNSTYDGLLYNTTWIKETLD--VPSIHF 329 Query: 336 DSAWVGYEQFIPMMKDSSPLLLNLGPDDPG--ILVTQSTHKQQAGFSQASQIHKKDSHIK 393 DSAWV Y F P+ + S + G PG I TQSTHK A SQAS IH K S+ Sbjct: 330 DSAWVPYTHFHPIYQGKSGM---SGDRIPGKVIFETQSTHKMLAALSQASLIHIKGSY-- 384 Query: 394 GQKRYINHKQFNNAYMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKN 453 + FN A+M +STSP YP+ A+++ A M G +G++L ++ +++ RK Sbjct: 385 ------DEDTFNEAFMMHTSTSPSYPIVASIETAAAMLRGNSGRRLIQRSIERALDFRKE 438 Query: 454 LLKNATMIKPFLPPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPN 513 + + + + WQ + V + W G +WHGF D+ F+DP Sbjct: 439 VQRLREESDGWFFDI-----WQPEE----VGEAQCWPVSPGEQWHGFQDADDDHMFLDPV 489 Query: 514 KFMLTTPGIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDN 573 K + TPG+D E G + GIPA ++A +L E G++ EK ++LFL + + + Sbjct: 490 KVTILTPGMD-EQGNMDSEGIPAALVAKFLDERGVVVEKTGPYNLLFLFSIGIDKTRAMG 548 Query: 574 LVTQIVKFESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKE 633 L+ + +F+ + + +LP LY+E D Y I+ L Q +H + + + Sbjct: 549 LLRGLTEFKRSYDLNLRVKNMLPDLYAEDPDFYRNMRIQDLAQGIHRLIRQHQLSQLMLS 608 Query: 634 MFLGKYFPEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWT 693 F PE MTP+QA +K + + L ++ G + LPYPPG+ ++PGE Sbjct: 609 AF--DVLPEMKMTPHQAWQRQIKGEVETIELENLVGRISANMILPYPPGVPLLMPGEMIV 666 Query: 694 KVAQKY--FLILEESINR-FPGFAPEIQG 719 + ++ FL++ SI R +PGF +I G Sbjct: 667 EESRAVLNFLLMLCSIGRHYPGFETDIHG 695 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: 1225 Number of extensions: 63 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: 745 Length of database: 712 Length adjustment: 40 Effective length of query: 705 Effective length of database: 672 Effective search space: 473760 Effective search space used: 473760 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