Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BPHYT_RS04980 BPHYT_RS04980 lysine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__BFirm:BPHYT_RS04980 Length = 761 Score = 406 bits (1043), Expect = e-117 Identities = 246/702 (35%), Positives = 366/702 (52%), Gaps = 36/702 (5%) Query: 39 NRTVVDADNSDFVDVAAVVVMDDEKAIINKADETKFNIPIFII--TDDSSKVDGETMSKI 96 + VV+ + + AA+V + +A + + +IPIF+ T S + + + ++ Sbjct: 74 DNVVVEGETPELA--AAIVAL---RAFVTEVRRRNADIPIFLYGETRTSRHLPNDILREL 128 Query: 97 FHIIDWHNNYDRRLYDREIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYF 156 I + R I K Y D + PPFFK L Y + G+ + CPGH GG F Sbjct: 129 HGFIHMFEDTPE-FVARHIIRETKVYLDSLAPPFFKELVQYADEGSYSWHCPGHSGGVAF 187 Query: 157 RKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMN 216 KSP G+ F+ F+GEN+ R+D+CNA +LG LL H GP +E++AAR+F+AD +FV N Sbjct: 188 LKSPLGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFSADHVFFVTN 247 Query: 217 GTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYS 276 GT+TSN I VAPGD+VL DRN HKS+ + A+ G PV+L +R+++G IG I Sbjct: 248 GTSTSNKIVWHGTVAPGDIVLVDRNCHKSILH-AITMTGAIPVFLTPTRNNFGIIGPIPR 306 Query: 277 KDFDEKSIREKI-AKVDPEKAKAKRPF---RLAVIQLGTYDGTIYNAKQVVERIGHLCDY 332 +F+ ++I++KI A +A AK P R+ I TYDG IYN + + E +G D Sbjct: 307 SEFEPENIKKKILANPFAREALAKNPNLKPRILTITQSTYDGVIYNVEMIKEMLGDWLDT 366 Query: 333 ILFDSAWVGYEQFIPMMKDSSPLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHI 392 + FD AW+ + +F +D + + T STHK AG SQASQI +DS Sbjct: 367 LHFDEAWLPHAEFHEFYQDMHAIGAGRPRIGAMVFATHSTHKLLAGISQASQIVVQDSK- 425 Query: 393 KGQKRYINHKQFNNAYMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARK 452 R+ H+ FN AY+ +STSP Y + A+ D+ A M E G L +++ +++ R+ Sbjct: 426 --NSRFDKHR-FNEAYLMHTSTSPQYAIIASCDVAAAMMEAPGGPALVEESIAEALDFRR 482 Query: 453 NLLKNATMIKPFLPPVVHGKPW------QDADTEKIVSDIDYWKFEKGAKWHGFDGYADN 506 ++K +G W D E+ + + W +WHGF ADN Sbjct: 483 AMIK---------VDAEYGDDWFFKVWGPDQFAEEGIGSREDWMLRPNDEWHGFGPLADN 533 Query: 507 QYFVDPNKFMLTTPGIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAE 566 +DP K + TPG+D+ G + + GIPA I+ YL EHGII EK L S + T Sbjct: 534 FNMLDPIKATIVTPGLDM-GGGFGETGIPAAIVTKYLAEHGIIVEKTGLYSFFIMFTIGI 592 Query: 567 TQAKMDNLVTQIVKFESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNN 626 T+ + +++VT++ +F+ + PL VLP S H YE ++ LCQ++H Y+ N+ Sbjct: 593 TKGRWNSMVTELQQFKDDYDNNQPLWRVLPEFVS-HHPMYERVGLRDLCQQIHSVYRAND 651 Query: 627 TKEYQKEMFLGKYFPEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCI 686 EM+L E AM P A +L VP+ ++EG PYPPGI + Sbjct: 652 IARLTTEMYLSSM--EPAMKPSDAFAKLAHREIDRVPIDELEGRVTSILLTPYPPGIPLL 709 Query: 687 VPGEKWTKVAQKYFLILEESINRFPGFAPEIQGVYFEKENGK 728 +PGE++ K Y E RFPGF +I G+ E NG+ Sbjct: 710 IPGERFNKTIVNYLRFAREFNERFPGFHTDIHGLVGETINGR 751 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: 1292 Number of extensions: 71 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: 761 Length adjustment: 40 Effective length of query: 705 Effective length of database: 721 Effective search space: 508305 Effective search space used: 508305 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