Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate 8502206 DvMF_2916 Aromatic-L-amino-acid decarboxylase (RefSeq)
Query= BRENDA::Q9L072 (480 letters) >FitnessBrowser__Miya:8502206 Length = 510 Score = 188 bits (478), Expect = 3e-52 Identities = 140/443 (31%), Positives = 205/443 (46%), Gaps = 25/443 (5%) Query: 40 TVDALSPRIDAIDLDEPLHDTAAVLDELEDVYLRDAVYFHHPRYLAHLNCPVVIPALLGE 99 T D L+ I + D E AVLD++ A HPR+LA + LG+ Sbjct: 43 TFDELAALIPS-DWPEAGAGAHAVLDDVARCIEPYATRIGHPRFLAWITTSPAPAGTLGD 101 Query: 100 AVLSAVNSSLDTWDQSAGGTLIERKLIDWTCARIGLGPAAD-------GVFTSGGTQSNL 152 V + +N + ++ T++E ++ W L AAD G SGGT +NL Sbjct: 102 IVCTGLNQAPLSFKGGPAATVLEHVVLGWLARLFDLPQAADEGMDGAGGTIVSGGTMANL 161 Query: 153 QALLLARE----EAKAEDFADLR----IFASEASHFSVRKSAKLLGLGPDAVVSIPVDRD 204 L +AR EA A + ++ S+ H S+ +SA LLGLG D V +IP D Sbjct: 162 MGLTVARHTHFPEAATRGLAGIGRIPVLYVSDQGHMSIERSAVLLGLGADNVRAIPSGAD 221 Query: 205 KRMQTVALARELERCARDGLVPMAVVATGGTTDFGSIDPLPEIAGLCEQYGVWMHVDAAY 264 RM AL + GL P VVA G+ G++DPLP+IA C G+W HVDAAY Sbjct: 222 NRMDVAALRAAITMDREAGLAPFCVVAQAGSVTTGAVDPLPDIADTCADEGLWFHVDAAY 281 Query: 265 GCGLLASLKYRDRITGIERADSVTVDYHKSFFQPVSSSAVLVRDAATLRHATY--HAEYL 322 G + + + R + GI RADS+ VD HK FF P+ L R A + AT+ A YL Sbjct: 282 GGAAMLTDEGRALLAGIHRADSICVDPHKWFFIPLECGVTLFRSKAQ-QLATFRARASYL 340 Query: 323 NPRRMVQERIPNQVDKSLQTTRRFDALKLWMTLRVMGADGIGVLFDEVCDLAAEGWKLLA 382 +E + + + +R ALK+W R G + + + +LA L A Sbjct: 341 G-----EENPHDLKNTTFILSRANRALKVWFAFRTYGRERLRRIVTRNMELARHFRDLCA 395 Query: 383 ADPRFDVVVQPSLSTLVFRHIP-ADVTDPAEIDRANLYARKALFASGDAVVAGTKVAGRH 441 A P + V+ LS R++P ++DR + + L ASG+ + V GR Sbjct: 396 ASPEWRVLAPVQLSIACARYVPQGGGWTEEDVDRLQVRLLERLEASGEGFLTPAMVRGRA 455 Query: 442 YLKFTLLNPETTPADIAAVLDLI 464 ++ + N T+ ADI + DL+ Sbjct: 456 GVRLCVANHRTSEADIRLLFDLM 478 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: 618 Number of extensions: 33 Number of successful extensions: 4 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: 510 Length adjustment: 34 Effective length of query: 446 Effective length of database: 476 Effective search space: 212296 Effective search space used: 212296 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