Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate AZOBR_RS00105 AZOBR_RS00105 ornithine decarboxylase
Query= SwissProt::B4XMC6 (405 letters) >FitnessBrowser__azobra:AZOBR_RS00105 Length = 378 Score = 130 bits (326), Expect = 8e-35 Identities = 116/367 (31%), Positives = 177/367 (48%), Gaps = 25/367 (6%) Query: 9 QTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVS 68 Q +TP + D D ++ + + +EA K I YA+KAN IL LL L S D S Sbjct: 12 QRPQTPCLVVDLDVVEANYHDLEEALPDAK--IFYAVKANPAPEILGLLTRLGSAFDTAS 69 Query: 69 IGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGI 128 + EIQ L AG P RI + K +I +A +L + +S EL+ I A Sbjct: 70 VPEIQMVLAAGCAPERISYGNTIKKEADIRRAFELGVRLFAFDSEAELEKIARAAPG--- 126 Query: 129 KARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGS 188 AR+ RI + + P KFG A E+ L AK + P V FH+GS Sbjct: 127 -ARVFCRILTSGEGAEWPL------SRKFGCDLAMARELLLKAKGMNVV-PYGVSFHVGS 178 Query: 189 QLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNA 248 Q DL A +VA++ + L LG+DL ++GGG Y + + Y Q I + Sbjct: 179 QQKDLMQWDHAIFQVAQLFRELEVLGVDLGMINLGGGFPTRYRT-DVPETTAYGQAIFES 237 Query: 249 LQ---GLDL-TIICEPGRSIVAESGELITQ-VLYEKKAQN--KRFVIVDAGMNDFLRPSL 301 L+ G L I EPGRS+V +G + ++ VL +K+ N KR+V +D G L ++ Sbjct: 238 LRTHFGNRLPEAIVEPGRSMVGNAGIIESEVVLVSRKSANDVKRWVYLDIGKFSGLAETM 297 Query: 302 YHA-KHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAH--LP-ELEPGDKIAIEKVGA 357 A ++ I+V+ + + GP C+S+D + A LP +L+ GD++ I GA Sbjct: 298 DEAIQYPIQVMGDDGEGDSEAVVLAGPTCDSADVLYERAEYKLPMDLKAGDRVRIHATGA 357 Query: 358 YGSSMAS 364 Y ++ ++ Sbjct: 358 YTTTYSA 364 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: 326 Number of extensions: 15 Number of successful extensions: 3 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: 378 Length adjustment: 31 Effective length of query: 374 Effective length of database: 347 Effective search space: 129778 Effective search space used: 129778 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: 50 (23.9 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