Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate SMa2402 SMa2402 RhsB L-2,4-diaminobutyrate decarboxylase
Query= BRENDA::Q9L072 (480 letters) >FitnessBrowser__Smeli:SMa2402 Length = 495 Score = 330 bits (847), Expect = 5e-95 Identities = 192/458 (41%), Positives = 262/458 (57%), Gaps = 4/458 (0%) Query: 14 YRRSVTEGVERVAAKLATTDRPFTGVTVDALSPRIDAID-LDEPLHDTAAVLDELEDVYL 72 +R ++ + ++ V + A ++G + L ID +D L E AA L E+ L Sbjct: 33 FRNAMLQAIDMVVDQTAAASSLYSGTSFQGLRGLIDDLDPLPEVGTGIAAALAEIGRPAL 92 Query: 73 RDAVYFHHPRYLAHLNCPVVIPALLGEAVLSAVNSSLDTWDQSAGGTLIERKLIDWTCAR 132 A+ HP +AHL+CPV +PAL E ++SA N SLD+WDQS TL+E +++ Sbjct: 93 EHAMVVGHPAAMAHLHCPVAVPALAAEVLISATNQSLDSWDQSPFATLVEERVLACLTQL 152 Query: 133 IGLGPAADGVFTSGGTQSNLQALLLAREEAKAEDFADLRIFASEASHFSVRKSAKLLGLG 192 L +A G FTSGGTQSN+ AL LA + + S +HFS+RKSA +LG Sbjct: 153 AELPASASGNFTSGGTQSNMTALYLAAVRCGPDARKAGVVLTSAHAHFSIRKSAAILGFA 212 Query: 193 PDAVVSIPVDRDKRMQTVALARELERCARDGLVPMAVVATGGTTDFGSIDPLPEIAGLCE 252 DAV++I D D RM AL EL R A +G +P+AVVAT GTTD G+IDPL EIA L Sbjct: 213 EDAVIAIAADADGRMSVPALKAELLRVAGEGRIPVAVVATAGTTDLGAIDPLVEIADLAA 272 Query: 253 QYGVWMHVDAAYGCGLLASLKYRDRITGIERADSVTVDYHKSFFQPVSSSAVLVRDAATL 312 VWMHVDAAYG GLL S ++R R+ G+E A S+T+D+HK FQP+S +L+RD A Sbjct: 273 AQNVWMHVDAAYGGGLLFS-RHRSRLEGLEHAHSITLDFHKMLFQPISCGVLLLRDRADF 331 Query: 313 RHATYHAEYLNPRRMVQERIPNQVDKSLQTTRRFDALKLWMTLRVMGADGIGVLFDEVCD 372 A+YLNP V PN V++S+QTTRR DALK+ MT+R +G DG+ L + Sbjct: 332 APLASKADYLNPEDAVFADAPNLVERSMQTTRRADALKILMTMRAIGRDGLDALICQTLQ 391 Query: 373 LAAEGWKLLAADPRFDVVVQPSLSTLVFRHIPADVTDPAEIDRANLYARKALFASGDAVV 432 + + + PSLST++FR++ A P D L R ALF +G A + Sbjct: 392 NTHAAAEAVKTREYLSLAGPPSLSTVLFRYVSA--RGPKFADAITLKTRAALFNAGIAAL 449 Query: 433 AGTKVAGRHYLKFTLLNPETTPADIAAVLDLIAGHAEQ 470 A T + GR + K TLLNP +TP + +LD I A + Sbjct: 450 ATTVLDGRVHFKLTLLNPRSTPDVVHRILDAIGETARE 487 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: 625 Number of extensions: 34 Number of successful extensions: 5 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: 495 Length adjustment: 34 Effective length of query: 446 Effective length of database: 461 Effective search space: 205606 Effective search space used: 205606 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