Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_052473538.1 SUTH_RS10670 hypothetical protein
Query= curated2:O27390 (428 letters) >NCBI__GCF_000828635.1:WP_052473538.1 Length = 461 Score = 135 bits (340), Expect = 3e-36 Identities = 138/430 (32%), Positives = 185/430 (43%), Gaps = 38/430 (8%) Query: 19 DAVELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACKANTNLAVMRILEEE 78 D L E+G+PL+++ E +R YR F+ V Y+ K N AV IL +E Sbjct: 40 DVKGLLREFGSPLFILSEKMLRAQYRSFRDTFAAPGIDTVVAYSYKTNYLPAVCSILHQE 99 Query: 79 GSGIDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVRINVDSRSQLLRLSE 138 G+ + VS E A G +I++ G R +EL A+ INVD +L L Sbjct: 100 GAWAEVVSGMEYDLARSLGVPGGKIIFNGPYKRPEELARAIKEEALINVDGFDELDMLIS 159 Query: 139 IAPEGLRISFRVNPLVGAGHHEHCITGGEMSKFGVM--EREAPE----VYRMAMDLGFEP 192 A L I+ R + H T KFGV EA E + + L FE Sbjct: 160 -AARNLGIAARTGLRINFQHGRQSWT-----KFGVNADNGEALEALHRIKKAGKSLHFE- 212 Query: 193 VGIHAHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFGGGLGIPYTPEEEP-L 251 +H H G+ +PE + A + L+ +A R G+E DFGG G P +P Sbjct: 213 -ALHNHSGTFQTNPEIYSRAAQVLIGVA-RAARTMGLEPAIADFGG--GYPSNNRLKPGF 268 Query: 252 DI-----------DEFASKITGLFKDKLSEYGLGRPMMCLEPGRYIVGDASYLLTRVNTI 300 D+ FA I G +G RP M LEPGR +V A L V Sbjct: 269 DVAGGSGSSGQFLAPFAEAIVGPLSKARKAFG-ARPTMVLEPGRALVDAAFRLACSVVAR 327 Query: 301 KE--SYRKFAGVDAGFNTLLRPAMYGSYHHILVA-ERPLDEPSEKMDVA--GNVCESGDL 355 K + VDAG N L P Y H I A R + E + VA G +C D+ Sbjct: 328 KNIAGQGEAVIVDAGVNLL--PTAYWYDHRINAASSRDMQEAAGAKPVAVFGPLCMQVDV 385 Query: 356 FARDRQLPEINEGDVLAIMNAGAYSFSMSSQYNSRPRPAEVLVREGKVDVVRERETFSDL 415 LP ++ G L I N GAY + S Q+ +PRPA VL+ V+ +R RET SD+ Sbjct: 386 LRERAVLPNLSLGSPLMISNVGAYCITQSMQF-IQPRPAVVLLGPRGVEEIRRRETRSDI 444 Query: 416 LRGQNVPARL 425 VPARL Sbjct: 445 FDMDRVPARL 454 Lambda K H 0.320 0.140 0.408 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: 492 Number of extensions: 28 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: 428 Length of database: 461 Length adjustment: 32 Effective length of query: 396 Effective length of database: 429 Effective search space: 169884 Effective search space used: 169884 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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