Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate 8499899 DvMF_0664 Orn/DAP/Arg decarboxylase 2 (RefSeq)
Query= curated2:O27390 (428 letters) >FitnessBrowser__Miya:8499899 Length = 474 Score = 142 bits (359), Expect = 2e-38 Identities = 119/442 (26%), Positives = 192/442 (43%), Gaps = 46/442 (10%) Query: 6 EVNDKGHLL-IGGADAVELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACK 64 +V D+G +L +GG LA +YGTPL V+D +R + + A + Y+ K Sbjct: 31 DVTDEGGVLAVGGMPCTRLARDYGTPLLVVDAAALRRRVQDVQAALDEVLPGAMLAYSYK 90 Query: 65 ANTNLAVMRILEEEGSGIDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVR 124 N ++R+L + G G + +SP E + + G D +++Y G + + + A+ G Sbjct: 91 TNCIPGILRMLHDAGVGAEVISPYEYWLSESLGVDGGQVVYNGVDKSRESIARAVARGTL 150 Query: 125 INVDSRSQLLRLSEIAPE-------GLRISFRVNPLVGAGHHEHCITGGEMSKFGVMERE 177 +N+DSR ++ + A E GLR++ + G G +++ + Sbjct: 151 VNIDSRDEVDVVLAAAREQRRTARVGLRLALNRSAQFGLDPE-----GDDLAHVVRNCLD 205 Query: 178 APEVYRMAMDLGFEPVGIHAHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFG 237 AP+ DL V +H ++ S + +D+ + GV +D G Sbjct: 206 APD----HADL----VALHFNVTSNARHSGYHARCLSRALDVMSWLAREHGVRIRLLDVG 257 Query: 238 GGLGI--------------------PYTPEEEPL-DIDEFASKITGLFKDKLSEYGLGRP 276 GG G+ P +P D + + + ++ L P Sbjct: 258 GGFGVETSKNMSGAEYGLYRLFGVQPGAAWMDPFQDFRLYLRDLADTLRAFCAQNDLPVP 317 Query: 277 MMCLEPGRYIVGDASYLLTRVNTIKE--SYRKFAGVDAGFNTLLRPAMYGSYHHILVAER 334 +C+EPGR + A LLT+V +KE FA DAG + P + +H +A Sbjct: 318 GVCIEPGRLLTSKAELLLTQVKAVKERPGAEPFAITDAGRLSQAFPCDF-EWHEAFLASD 376 Query: 335 PLDEPSEKMDVAGNVCESGDLFARDRQLPEINEGDVLAIMNAGAYSFSMSSQYNSRPRPA 394 PS V G VC D R + LPE+ GDVLA+M+AGAY FS + + PR A Sbjct: 377 LRRPPSRPYTVTGRVCTRSDWLYRGKLLPELATGDVLAVMDAGAY-FSSYAMNFAFPRAA 435 Query: 395 EVLVREGKVDVVRERETFSDLL 416 V V +G+ V+R RE F L+ Sbjct: 436 VVAVEDGRARVLRRREDFRHLV 457 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: 572 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 428 Length of database: 474 Length adjustment: 33 Effective length of query: 395 Effective length of database: 441 Effective search space: 174195 Effective search space used: 174195 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 Aug 03 2021. The underlying query database was built on Aug 03 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