Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate PP_4140 PP_4140 lysine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__Putida:PP_4140 Length = 749 Score = 373 bits (957), Expect = e-107 Identities = 220/621 (35%), Positives = 329/621 (52%), Gaps = 28/621 (4%) Query: 113 REIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGEN 172 R++ AA Y DG+LPPFFKAL + + N + PGH GG + KSP G+ F+ F+GEN Sbjct: 134 RQVARAAHTYLDGLLPPFFKALVQHTAQSNYSWHTPGHGGGVAYHKSPVGQAFHQFFGEN 193 Query: 173 IFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAP 232 RSD+ + +LG LL H GP +AE AAR F AD T+FV+NGT+T+N I A V Sbjct: 194 TLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIVWHAMVGR 253 Query: 233 GDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVD 292 DLVL DRN HKSV + A++ G P+YL R+ G IG I +F ++I KI + + Sbjct: 254 DDLVLVDRNCHKSVVH-AIIMTGAIPLYLCPERNELGIIGPIPLSEFSPEAIAAKI-QAN 311 Query: 293 PEKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDS 352 P + +LAV+ TYDG Y+A + + +G + + FD AW Y F Sbjct: 312 PLARDRGQRIKLAVVTNSTYDGLCYHAGLIKQALGASVEVLHFDEAWFAYAAFHDFFTGR 371 Query: 353 SPLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFS 412 + D P + T STHK A FSQAS IH +D G +R ++ +FN A+M Sbjct: 372 YAMGTACAADSPLVFSTHSTHKLLAAFSQASMIHVQD----GARRQLDRDRFNEAFMMHI 427 Query: 413 STSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSV-------NARKNLLKNATMIKPFL 465 STSP Y + A+LD+ + M EG AG+ L + ++ N R+++ + Sbjct: 428 STSPQYSILASLDVASTMMEGPAGRSLLQEMFDEALSFRRALANLREHIAAADWWFSIWQ 487 Query: 466 PPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVE 525 PP G P A W + GA+WHGF + +DP K L PG+ + Sbjct: 488 PPSAEGIPRLAAQD---------WLLQPGAQWHGFGEVVTDYVLLDPLKVTLVMPGLSAD 538 Query: 526 TGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLV 585 G GIPA +++ +L E G++ EK L S L L + T+ K L+T++++F+ Sbjct: 539 -GVLGARGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTELLEFKRHY 597 Query: 586 KADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAM 645 + PL LP + + RY+G ++ LC ++HD Y+ N T + K +F PE A+ Sbjct: 598 DGNTPLSSCLPSVGAADALRYQGMGLRDLCDQLHDCYRANATAKQLKRLF--TRLPEVAV 655 Query: 646 TPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKY--FLIL 703 +P QA ++++ + VP+ + G A +PYPPGI I+PGE++T+ + +L Sbjct: 656 SPAQAYDKMVRGEVEAVPIEALLGRVAAVMLVPYPPGIPLIMPGERFTEATRSILDYLAF 715 Query: 704 EESINR-FPGFAPEIQGVYFE 723 + N+ FPGF ++ G+ E Sbjct: 716 ARAFNQGFPGFVADVHGLQHE 736 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: 1123 Number of extensions: 50 Number of successful extensions: 7 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: 749 Length adjustment: 40 Effective length of query: 705 Effective length of database: 709 Effective search space: 499845 Effective search space used: 499845 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