Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate H281DRAFT_00160 H281DRAFT_00160 ornithine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__Burk376:H281DRAFT_00160 Length = 761 Score = 400 bits (1027), Expect = e-115 Identities = 242/687 (35%), Positives = 358/687 (52%), Gaps = 34/687 (4%) Query: 54 AAVVVMDDEKAIINKADETKFNIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLY 111 AA+V + +A + + +IPIF+ T S + + + ++ I + Sbjct: 87 AAIVAL---RAFVTEVRRRNADIPIFLYGETRTSRHLPNDILRELHGFIHMFEDTPE-FV 142 Query: 112 DREIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGE 171 R I K Y D + PPFFK L Y + G+ + CPGH GG F KSP G+ F+ F+GE Sbjct: 143 ARHIIRETKVYLDSLAPPFFKELVQYADEGSYSWHCPGHSGGVAFLKSPLGQMFHQFFGE 202 Query: 172 NIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVA 231 N+ R+D+CNA +LG LL H GP +E++AAR+F+AD +FV NGT+TSN I VA Sbjct: 203 NMLRADVCNAVDELGQLLDHTGPVAASERNAARIFSADHVFFVTNGTSTSNKIVWHGTVA 262 Query: 232 PGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKI-AK 290 PGD+VL DRN HKS+ + A+ G PV+L +R+++G IG I +F+ ++IR KI A Sbjct: 263 PGDIVLVDRNCHKSILH-AITMTGAIPVFLTPTRNNFGIIGPIPRSEFEPENIRRKIEAN 321 Query: 291 VDPEKAKAKRPF---RLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIP 347 +A AK P R+ I TYDG IYN + + E +G D + FD AW+ + +F Sbjct: 322 PFAREALAKNPDLKPRILTITQSTYDGVIYNVEMIKEMLGEWLDTLHFDEAWLPHAEFHE 381 Query: 348 MMKDSSPLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNA 407 +D + + T STHK AG SQASQI +DS R+ H+ FN A Sbjct: 382 FYQDMHAIGAGRPRIGAMVFATHSTHKLLAGISQASQIVVQDSK---NSRFDKHR-FNEA 437 Query: 408 YMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPP 467 Y+ +STSP Y + A+ D+ A M E G L +++ +++ R+ + K T Sbjct: 438 YLMHTSTSPQYAIIASCDVAAAMMEAPGGTALVEESIAEALDFRRAMTKVDT-------- 489 Query: 468 VVHGKPW------QDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPG 521 +G W D ++ + + W WHGF A+ +DP K + TPG Sbjct: 490 -EYGDDWFFKVWGPDQFADEGIGSREDWMLRPNDSWHGFGPLAEGFNMLDPIKATIVTPG 548 Query: 522 IDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKF 581 +D++ G + + GIPA I+ YL EHGII EK L S + T T+ + +++VT++ +F Sbjct: 549 LDMD-GGFGETGIPAAIVTKYLAEHGIIVEKTGLYSFFIMFTIGITKGRWNSMVTELQQF 607 Query: 582 ESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFP 641 + + PL VLP + H YE ++ LCQ++H Y+ N+ EM+L Sbjct: 608 KDDYDNNQPLWRVLPDFVALH-PTYERVGLRDLCQQIHSVYRANDIARLTTEMYLSSM-- 664 Query: 642 EQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFL 701 E AM P A +L VP+ ++EG PYPPGI ++PGE++ K Y Sbjct: 665 EPAMKPSDAFAKLAHREIDRVPIDELEGRVTSILLTPYPPGIPLLIPGERFNKTIVNYLR 724 Query: 702 ILEESINRFPGFAPEIQGVYFEKENGK 728 E RFPGF +I G+ E NG+ Sbjct: 725 FAREFNERFPGFHTDIHGLVGEMINGR 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: 1282 Number of extensions: 73 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