Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate HSERO_RS13690 HSERO_RS13690 diaminopimelate decarboxylase
Query= curated2:Q9PII5 (402 letters) >FitnessBrowser__HerbieS:HSERO_RS13690 Length = 418 Score = 146 bits (369), Expect = 1e-39 Identities = 110/367 (29%), Positives = 184/367 (50%), Gaps = 21/367 (5%) Query: 12 TPFYIYNFDFIKERFLNLKEAFKARKSQIFYAVKANSNLSLLQMLANLDSGFDCVSIGEV 71 TPFY+Y+ ++ R +L+ A + + Y++KAN +L+Q +A L GFD S GE+ Sbjct: 41 TPFYVYDRALLRARVAHLRAHLPAELA-LHYSIKANPMPALVQAMAQLVDGFDVASGGEL 99 Query: 72 KRALKAGAKAYKIIFSGVGKTKEELRQALEYDILYINLESEAEMMLLESVAKELNLKARI 131 AL I F+G GK+ ELR+AL ++ +++ESE E + ++A+EL ++ + Sbjct: 100 ATALDTPMPVQHISFTGPGKSLAELRRALAAGVM-LHVESEREAEAVAALAQELGVRPGV 158 Query: 132 SIRVNPNVDAKTHPYISTGLNENKFGVEIDIARKMYLYAKNSSFLEPVGVHFHIGSQLLD 191 ++R+NP + K+ + G FGV+ + A + + ++ G+ GSQ LD Sbjct: 159 TLRINPPFELKSSG-MRMGGGAKPFGVDAEAAPALLRWLAGQG-VQVAGLQIFCGSQSLD 216 Query: 192 ISPIHEAAAIVAKLVRELKA-LQIDLKFFDIGGGLGVAYEKNECEPDLYDYAQGI---LA 247 I A + +L +L + L+ +IGGG G+ Y E ++ + L Sbjct: 217 AQAIMAAQSSSFELALQLAGEAGLSLRVLNIGGGFGIPYFPGERALEIAPIGAHLAQWLP 276 Query: 248 QLHGL--DLTIGMEPGRYLVAKSGEFVCSVLYEKQNKTKRFVVVDGAMNDLIRPS----- 300 +L L L + ME GRYLV ++G +V V+ KQ++ + F+VVDG ++ + S Sbjct: 277 RLRALHPQLRVVMEMGRYLVGEAGLYVSRVIDRKQSRGEVFLVVDGGLHHHLAASGNFGQ 336 Query: 301 -LYEAYHEIILPYNQ-----GEESLCDVVGGICESGDFFAKARSLPSTQSDDIMVIKNTG 354 + + Y I+P G VVG +C D A LP+ D++V+ +G Sbjct: 337 VIRKNYPVTIVPQQPQRSGGGTTERVSVVGPLCTPLDVLAAQMLLPAAAVGDLVVVFQSG 396 Query: 355 AYGFSMS 361 AYG S S Sbjct: 397 AYGLSAS 403 Lambda K H 0.319 0.137 0.385 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: 19 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: 402 Length of database: 418 Length adjustment: 31 Effective length of query: 371 Effective length of database: 387 Effective search space: 143577 Effective search space used: 143577 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: 50 (23.9 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