Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate WP_011842694.1 RSPH17029_RS19415 D-amino acid dehydrogenase
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >NCBI__GCF_000015985.1:WP_011842694.1 Length = 436 Score = 547 bits (1409), Expect = e-160 Identities = 269/416 (64%), Positives = 323/416 (77%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 MR++VLG+GV+GV++AY LA+AGHEVTVVDRQP ALETS+ANAGE+SPGY++PWAAPG+ Sbjct: 1 MRIVVLGAGVVGVTSAYELARAGHEVTVVDRQPAAALETSFANAGEISPGYASPWAAPGI 60 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 AKA++WM MKH+PLVIRP++D A + L +L N +Y NKGRMVRLAEYSRDCL Sbjct: 61 PAKALRWMFMKHAPLVIRPRLDAAQVRFLLAILRNCTPAAYAQNKGRMVRLAEYSRDCLT 120 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 LR TG+ +DER +GTLQ+FR+QKQ+DAAA D+ VL VP+ LLD +GC A EP LR Sbjct: 121 DLRATTGLAFDERQQGTLQLFRSQKQLDAAARDIEVLRAGGVPFELLDADGCLAAEPGLR 180 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTD 240 +++I GGL L GDETGDCF+FT LA +A E GV FRY TG+ +L +G RVTGV T Sbjct: 181 AARDRIAGGLRLTGDETGDCFKFTQGLAGLAEEGGVRFRYGTGVERLRVEGGRVTGVETT 240 Query: 241 AGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDETHKI 300 GT AD+ VVA+GSYSP LV P GL LPVYPVKGYS+T+PIVDA AP STVMDET+KI Sbjct: 241 KGTFLADAVVVALGSYSPALVAPLGLRLPVYPVKGYSITVPIVDAERAPVSTVMDETYKI 300 Query: 301 AVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAEFWTGLRPNTP 360 A+TRLG RIRVGG AE+ GF TL P RR L V+DLF GDLS+A FWTGLRP TP Sbjct: 301 AITRLGTRIRVGGMAEVAGFSATLPPARRETLAMSVNDLFGGAGDLSRASFWTGLRPMTP 360 Query: 361 DGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGGRQTEIDMDGLTVARY 416 DGTP+VG TPV L+LNTGHGTLGWTMAAGS RV++D++ GR EI+ L + RY Sbjct: 361 DGTPVVGRTPVAGLWLNTGHGTLGWTMAAGSARVLSDLIDGRAPEIESADLGIERY 416 Lambda K H 0.319 0.136 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: 663 Number of extensions: 27 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: 436 Length of database: 436 Length adjustment: 32 Effective length of query: 404 Effective length of database: 404 Effective search space: 163216 Effective search space used: 163216 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 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