Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate RR42_RS15940 RR42_RS15940 lysine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__Cup4G11:RR42_RS15940 Length = 754 Score = 418 bits (1074), Expect = e-121 Identities = 254/707 (35%), Positives = 378/707 (53%), Gaps = 35/707 (4%) Query: 42 VVDADNSDFV---DVAAVVVMDDEKAIINKADETKFNIPIFII--TDDSSKVDGETMSKI 96 +V D+ +FV D ++ +A +N+ ++PIF+ T S + + + ++ Sbjct: 61 IVSIDDDEFVSEDDRPEAAAIEKLRAFVNEVRRRNTDLPIFLYGETRTSRHIPNDILREL 120 Query: 97 FHIIDWHNNYDRRLYDREIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYF 156 I + R I A+ Y D + PPFFKAL AY + + + CPGH GG F Sbjct: 121 HGFIHMFEDTPE-FVARHIIREARVYLDSLAPPFFKALIAYAQDSSYSWHCPGHSGGVAF 179 Query: 157 RKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMN 216 KSP G+ F+ F+GEN+ R+D+CNA +LG LL H GP +E++AAR+FN+D YFV N Sbjct: 180 LKSPVGQVFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNSDHMYFVTN 239 Query: 217 GTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYS 276 GT+TSN + A VAPGD+V+ DRN HKS+ + A++ G PV+L +R+ YG IG I Sbjct: 240 GTSTSNKMVWHANVAPGDIVVVDRNCHKSILH-AIMMTGAIPVFLMPTRNHYGIIGPIPK 298 Query: 277 KDFDEKSIREKIAKVD-PEKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILF 335 +FD ++IR KIA +AK ++P R+ I GTYDG +YNA+Q+ E + D + F Sbjct: 299 SEFDPETIRRKIAAHPFASQAKNQKP-RILTITQGTYDGVLYNAEQIKEMLATEIDTLHF 357 Query: 336 DSAWVGYEQFIPMMKDSSPLLLNLGPDDPG-----ILVTQSTHKQQAGFSQASQIHKKDS 390 D AW+ + F D + +G D P + TQSTHK AG SQASQI +DS Sbjct: 358 DEAWLPHAAF----HDFYHNMHAIGRDRPRSKDALVFATQSTHKLLAGLSQASQILVQDS 413 Query: 391 HIKGQKRYINHKQFNNAYMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNA 450 + RY +FN AY+ +STSP Y + A+ D+ A M E G L +++ +++ Sbjct: 414 DTRKLDRY----RFNEAYLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESIQEAMDF 469 Query: 451 RKNLLKNATMIKPFLPPVVHGKPW-----QDADTEKIVSDIDYWKFEKGAKWHGFDGYAD 505 R+ + K ++ +G W +A E + D + W + +WHGF AD Sbjct: 470 RRAMRK----VEGDYDAGNNGDWWFKVWGPEALAEDDIGDREEWMLKANERWHGFGDLAD 525 Query: 506 NQYFVDPNKFMLTTPGIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPA 565 +DP K + TPG+DV+ GE+ D GIPA I+ YL EHGII EK L S + T Sbjct: 526 GFNLLDPIKATIITPGLDVD-GEFSDRGIPAAIVTKYLAEHGIIIEKTGLYSFFIMFTIG 584 Query: 566 ETQAKMDNLVTQIVKFESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNN 625 T+ + ++LVT++ +F+ + PL VLP +H +YE ++ LC +H YK N Sbjct: 585 ITKGRWNSLVTELQQFKDDYDQNQPLWRVLPEFVGKH-PQYEKLGLRDLCDAIHSVYKAN 643 Query: 626 NTKEYQKEMFLGKYFPEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFC 685 + EM+L E AM P A + + V + ++EG PYPPGI Sbjct: 644 DVARVTTEMYLSDM--EPAMKPSDAWAMMAHREIERVAVDELEGRVTAILLTPYPPGIPL 701 Query: 686 IVPGEKWTKVAQKYFLILEESINRFPGFAPEIQGVYFEKENGKSVAY 732 ++PGE++ ++ +Y E FPGF +I G+ E+ G AY Sbjct: 702 LIPGERFNRIIVQYLKFAREFNKLFPGFETDIHGLVEEEVEGGGKAY 748 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: 1314 Number of extensions: 58 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: 754 Length adjustment: 40 Effective length of query: 705 Effective length of database: 714 Effective search space: 503370 Effective search space used: 503370 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