Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate 200933 SO1769 glutamate decarboxylase, putative (NCBI ptt file)
Query= BRENDA::Q9L072 (480 letters) >FitnessBrowser__MR1:200933 Length = 533 Score = 164 bits (416), Expect = 5e-45 Identities = 130/499 (26%), Positives = 226/499 (45%), Gaps = 67/499 (13%) Query: 25 VAAKLATTDRPFTGVTVDALSPRIDAIDLDEPLHD-------TAAVLDELEDVYLRDAVY 77 + KL+ F G ++ AL + I+ D + + DE+ + +V+ Sbjct: 17 IEQKLSEDLAGFLGDSIAALEKPLSEIETDFQTFEIPNQPRFVSDYTDEIMQNLVAHSVH 76 Query: 78 FHHPRYLAHLNCPVVIPALLGEAVLSAVNSSLDTWDQSAGGTLIERKLI----------- 126 P ++ H+ + L ++ +N +L + S T +ER+++ Sbjct: 77 TAAPSFIGHMTSALPYFVLPLSKMMVGLNQNLVKIETSKAFTPLERQVLGMMHHLIYAQH 136 Query: 127 -DWTCARIGLGPAADGVFTSGGTQSNLQALLLAREEA-KAE------------------D 166 D+ + + G F SGGT +N+ AL +AR + KA+ D Sbjct: 137 DDFYRNWMHSANHSLGAFCSGGTVANITALWIARNQLLKADGDFKGVTREGLIKALRHYD 196 Query: 167 FADLRIFASEASHFSVRKSAKLLGLGPDAVVSIPVDRDKRMQTVALARELERCARDGLVP 226 + DL I SE H+S+ K+ LLG+G D ++SIP D D ++ + + A + Sbjct: 197 YDDLAILVSERGHYSLGKAVDLLGIGRDNIISIPTDADNKVDVTQMRKIAVELAHKRIKV 256 Query: 227 MAVVATGGTTDFGSIDPLPEIAGLCEQYGVWMHVDAAYGCGLLASLKYRDRITGIERADS 286 MA+V GTT+ G+IDPL ++A L + HVDAA+G L S KYR + G+E ADS Sbjct: 257 MAIVGVAGTTETGNIDPLKQLAALASELNCHFHVDAAWGGASLLSNKYRHLLDGVELADS 316 Query: 287 VTVDYHKSFFQPVSSSAVLVRDAATLRHATYHAEYLNPRRMVQERIPNQVDKSLQTTRRF 346 VT+D HK + P+ + VL ++ +HAEY+ ++ + ++L+ +R Sbjct: 317 VTIDAHKQMYVPMGAGMVLFKNPEFAHAIAHHAEYI-----LRRGSKDLGSQTLEGSRPG 371 Query: 347 DALKLWMTLRVMGADGIGVLFDEVCDLAAEGWKLLAADPRFDVVVQPSLSTLVFRHIPAD 406 A+ + L+++G DG +L + + A + + A P F++V P L L +R++PA Sbjct: 372 MAMLVHACLQIIGRDGYEILINNSLEKARYFAEQIDAHPDFELVTAPELCLLTYRYVPAS 431 Query: 407 VT----------DPAEIDRAN-------LYARKALFASGDAVVAGTKVAGRHY------- 442 V D A+++R N + +K G + V+ T++ Y Sbjct: 432 VQAAMQVAIEQGDKAKLERFNEQLDGLTQFIQKHQREQGKSFVSRTRIQPARYFRQPTVV 491 Query: 443 LKFTLLNPETTPADIAAVL 461 + L NP T+ + VL Sbjct: 492 FRVVLANPLTSHEILNQVL 510 Lambda K H 0.320 0.135 0.397 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: 543 Number of extensions: 19 Number of successful extensions: 3 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: 480 Length of database: 533 Length adjustment: 34 Effective length of query: 446 Effective length of database: 499 Effective search space: 222554 Effective search space used: 222554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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