Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_009562392.1 AFE_RS06870 biosynthetic arginine decarboxylase
Query= SwissProt::B4XMC6 (405 letters) >NCBI__GCF_000021485.1:WP_009562392.1 Length = 637 Score = 75.5 bits (184), Expect = 4e-18 Identities = 76/278 (27%), Positives = 129/278 (46%), Gaps = 45/278 (16%) Query: 28 LNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVF 87 L+YK +F Y +K N ++ + L +GA V L+AG KP + Sbjct: 87 LDYKGSFTP-----VYPIKVNQQRRVVEEI--LRAGAGSVG-------LEAGSKPELLAV 132 Query: 88 SGVGK-------SAFEIEQALKLNI--------LFLNVESFMELKTIETIAQSLGIKARI 132 G+ + ++ ++ ++L + ++L VE EL I A LG+K RI Sbjct: 133 IGLMPVGGTIICNGYKDKEYIRLALTGEKLGMQVYLVVEKPSELPLILNEASRLGVKPRI 192 Query: 133 SIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSV-HFHIGSQLL 191 +R A + + +TG +++KFG+ + LE+ + L+ + + HFH+GSQ+ Sbjct: 193 GVRARL-ASAGSGKWQNTGGEKSKFGLSTADILELVHRLRAENALDSLQLLHFHLGSQIP 251 Query: 192 DLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEET-------IKLYDYAQG 244 +++ I ++ A++ L LG L DVGGG+GV YE + + DYA Sbjct: 252 NIQFIRGGMRECARLYAELRRLGAALEVVDVGGGLGVDYEGTHSRAYCSTNYHVSDYAHA 311 Query: 245 ILNAL------QGL-DLTIICEPGRSIVAESGELITQV 275 I+ L +GL + II E GR++ A L+ V Sbjct: 312 IVATLADVSRQEGLPEPRIISESGRALTAHHAILVANV 349 Lambda K H 0.319 0.138 0.389 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: 477 Number of extensions: 20 Number of successful extensions: 1 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: 405 Length of database: 637 Length adjustment: 34 Effective length of query: 371 Effective length of database: 603 Effective search space: 223713 Effective search space used: 223713 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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