Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate Synpcc7942_2310 Synpcc7942_2310 conserved hypothetical protein, L-2,4-diaminobutyrate decarboxylase
Query= BRENDA::Q9L072 (480 letters) >FitnessBrowser__SynE:Synpcc7942_2310 Length = 489 Score = 197 bits (500), Expect = 9e-55 Identities = 141/416 (33%), Positives = 211/416 (50%), Gaps = 24/416 (5%) Query: 56 PLHDTAAVLDELEDVYLRDAVYFHHPRYLAHLNCPVVIPALLGEAVLSAVNSSLDTWDQS 115 PL D +L +LE + L A+ +P YL H++ +++G+A+ + +N++L + + S Sbjct: 65 PLPD---LLQQLEPL-LAQAMNPANPGYLGHMDPVASTASVIGDAIAALLNNNLLSVEMS 120 Query: 116 AGGTLIERKLIDWTCARIGLGPAADGVFTSGGTQSNLQALLLAREEAKAEDFADLR---- 171 + +E ++ R GLG A G+ SGG+ +NLQA+ LAR A L Sbjct: 121 PSFSRLETAVLRELAQRFGLGDEAGGLLLSGGSLANLQAIALARNWALQVQETGLAGLTQ 180 Query: 172 ---IFASEASHFSVRKSAKLLGLGPDAVVSIPVDRDKRMQTVALARELERCARDGLVPMA 228 +FASEA+H S++K+A LLGLG AV+ I DR RMQ AL + R G P Sbjct: 181 RPILFASEAAHTSIQKAAMLLGLGSQAVIPIATDRRGRMQVAALTEAIASARRQGQRPFC 240 Query: 229 VVATGGTTDFGSIDPLPEIAGLCEQYGVWMHVDAAYGCGLLASLKYRDRITGIERADSVT 288 +VAT GTT GSIDPLPE++ + G+W HVDA+YG ++ S +Y ++ GIE+A+SVT Sbjct: 241 LVATAGTTVTGSIDPLPELSAIARTEGLWFHVDASYGGAVIFSPRYAHKLQGIEQANSVT 300 Query: 289 VDYHKSFFQPVSSSAVLVRDAATLRHATYHAEYLNPRRMVQERIPNQVDKSLQTTRRFDA 348 + K +S+++L+RD + L T H P + + N + S+Q TR D Sbjct: 301 FNPQKWLCVAKTSASLLLRDWSLL---TEHFRIAAPYMGEADDLINLGEVSVQGTRPADI 357 Query: 349 LKLWMTLRVMGADGIGVLFDEVCDLAAEGWKLLAADPRFDVVVQPSLSTLVFRHIPADVT 408 LKLW+TL+ G G L + L L P+ V P L+ L FR +T Sbjct: 358 LKLWLTLQHFGDRGCAALVEHGLRLCRCFVAELRQRPQIQVATPPDLNILCFRLASDRLT 417 Query: 409 DPAEIDRANLYARKALFASGDAVVAGTKVAGRHYLKFTLLNPETTPADIAAVLDLI 464 + + Y +L + R +LK L+NP TTP I + I Sbjct: 418 AELQQFLLDRYFFLSL----------PRFRDRLWLKAVLVNPFTTPEHIRQLFGAI 463 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: 512 Number of extensions: 19 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: 489 Length adjustment: 34 Effective length of query: 446 Effective length of database: 455 Effective search space: 202930 Effective search space used: 202930 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