Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein
Query= SwissProt::Q9DBF1 (539 letters) >NCBI__GCF_000092045.1:WP_011425015.1 Length = 506 Score = 214 bits (544), Expect = 8e-60 Identities = 147/487 (30%), Positives = 233/487 (47%), Gaps = 24/487 (4%) Query: 50 DNEGVYNGSW-GGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNI--WADIP 106 D + + +G W G I P++ ++R S D E I A+KA++ W + Sbjct: 17 DFKMLIDGKWEAGASHPIERIAPSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMT 76 Query: 107 APKRGEIVRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGG 166 A +R I+ K D + + L L ++E GK + + GE+ VD+ YAA L+R + G Sbjct: 77 ASERSAILLKAADLIAARAEELAFLDAIEAGKPITQVRGEIAGSVDIWRYAAALARDLHG 136 Query: 167 PTLPSERPGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLV 226 + + G + + +G+V IIT +NFP + G AL G + K + TS Sbjct: 137 ESYNTLGDGTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTS-- 194 Query: 227 SVAVTKIIAQVLEDNLLPGAICSLVCG-GADIGTTMARDERVNLLSFTGSTQVGKEVALM 285 T ++ ++L+ +P + ++V G G ++G M V+++SFTGST VGK Sbjct: 195 --GSTLVLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKN 252 Query: 286 VQERFGKSLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNE 345 + K LELGG N I F DADL + + +F A AG+ C RL LH+SI ++ Sbjct: 253 AAQTLKKVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHKSIASD 312 Query: 346 VVDRLRSAYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMD-H 404 VV R+ ++VG+P DP G + T Q + V A+ G V +GG+ +D Sbjct: 313 VVRRVAELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGETLDLG 372 Query: 405 PGNYVEPTIVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKD- 463 G ++ PTI+ + D + +E F P+L V F+ E N + GLS+ ++++D Sbjct: 373 MGQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDF 432 Query: 464 -----LGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518 +GR R G + +N GA FGG K +G GRE G A + Y Sbjct: 433 DTCLTIGRSVR--------AGTIWMNTFMDGAS-ELPFGGYKQSGLGRELGRHAVEDYTE 483 Query: 519 RSTCTIN 525 T ++ Sbjct: 484 TKTLNMH 490 Lambda K H 0.319 0.137 0.421 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: 640 Number of extensions: 35 Number of successful extensions: 4 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: 539 Length of database: 506 Length adjustment: 35 Effective length of query: 504 Effective length of database: 471 Effective search space: 237384 Effective search space used: 237384 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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