Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate RR42_RS10745 RR42_RS10745 glutamate decarboxylase
Query= BRENDA::Q9L072 (480 letters) >FitnessBrowser__Cup4G11:RR42_RS10745 Length = 550 Score = 167 bits (423), Expect = 8e-46 Identities = 136/466 (29%), Positives = 216/466 (46%), Gaps = 60/466 (12%) Query: 50 AIDLDEPLHDTAAVLDELEDVYLRDAVYFHHPRYLAHL--NCPVVIPALLGEAVLSAVNS 107 +++L E A D L R + P ++ H+ + P +P+L V++A+N Sbjct: 67 SVELPETPTSPQAHADHLLHDVFRHVMPVASPTFVGHMTSSLPSFMPSLA--KVVAALNQ 124 Query: 108 SLDTWDQSAGGTLIERKLIDWTCARIGLGPAAD------------GVFTSGGTQSNLQAL 155 ++ + S T +ER++I + +A G SGGT +NL AL Sbjct: 125 NVVKLETSGALTGLERQVIGMLHKLVFAQDSAFYGRWLHDADHALGAICSGGTVANLTAL 184 Query: 156 LLAREE--AKAEDFAD-----------------LRIFASEASHFSVRKSAKLLGLGPDAV 196 +R + + FA L I SE H+S+RK+A +LG+G D + Sbjct: 185 WASRNKLLGACDGFAGIHRAGMVAALRHYGHDGLAIVVSERGHYSLRKAADVLGIGRDNL 244 Query: 197 VSIPVDRDKRMQTVALARELERCARDGLVPMAVVATGGTTDFGSIDPLPEIAGLCEQYGV 256 V + VD D RM+ L L R + PMA+V GTT+ G++DPL IA + ++ G Sbjct: 245 VPVAVDSDGRMRIDLLRDTLRDLQRRNIRPMAIVGIAGTTETGAVDPLDAIADVAQEAGC 304 Query: 257 WMHVDAAYGCGLLASLKYRDRITGIERADSVTVDYHKSFFQPVSSSAVLVRDAATLRHAT 316 HVDAA+G L S + R R GIERADSV +D HK F+ P+ + VL R A + Sbjct: 305 HFHVDAAWGGATLLSERERWRFAGIERADSVVIDAHKQFYVPMGAGMVLFRSPAWTQEII 364 Query: 317 YHAEYLNPRRMVQERIPNQVDKSLQTTRRFDALKLWMTLRVMGADGIGVLFDEVCDLAAE 376 HA Y+ V++ + +L+ +R A+ L+ L ++G G+ L D D A Sbjct: 365 QHANYI-----VRKGSVDLGRHTLEGSRGAAAVMLYANLHLLGRKGLAQLIDRSIDNARY 419 Query: 377 GWKLLAADPRFDVVVQPSLSTLVFRHIPADV-----TDPAE--------IDRANLYARKA 423 L+A P F++ +P L L +RH+P V T AE +D + ++ Sbjct: 420 FASLIARQPDFELNSRPQLCILTYRHVPETVHAALATACAERRDKILDALDALTISIQEM 479 Query: 424 LFASGDAVVAGTKVAGRHY-------LKFTLLNPETTPADIAAVLD 462 +G + V+ T++ + + L NP+TT A + +LD Sbjct: 480 QRDAGRSFVSRTQLMSAQWGGRPIAVFRVVLANPDTTHAILQDILD 525 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: 681 Number of extensions: 34 Number of successful extensions: 2 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: 550 Length adjustment: 35 Effective length of query: 445 Effective length of database: 515 Effective search space: 229175 Effective search space used: 229175 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