Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate H281DRAFT_03016 H281DRAFT_03016 aldehyde dehydrogenase (acceptor)
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Burk376:H281DRAFT_03016 Length = 483 Score = 218 bits (554), Expect = 5e-61 Identities = 144/458 (31%), Positives = 221/458 (48%), Gaps = 10/458 (2%) Query: 61 GRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDA 120 G GE PA EPIA V Q S AD + V+ AR A K+W I A +RG I+ ++ Sbjct: 22 GTGEYSVNINPATEEPIAHVAQGSAADVDTAVRAARAALKVWNGIKAAERGRILSRLAGL 81 Query: 121 LREKIQVLGSLVSLEMGKILVEGVGE-VQEYVDICDYAVGLSRMIGGPILPSERSGHALI 179 +R + L +L SL+ GK + + + V +D +Y G I G ++P R Sbjct: 82 MRANLDELAALESLDAGKPIAAVMRQDVPAAIDTLEYYAGWCDKINGQVVPV-RPDALTY 140 Query: 180 EQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLE 239 PVG+V I +NFP+ + W A A+ CG + K A T L ++ + ++ LE Sbjct: 141 TLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLSALRIGEL---ALE 197 Query: 240 DNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGG 299 PG + +T G +G A+ V+ ++FTGS VG+ + F R LELGG Sbjct: 198 AGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAGNFKRVTLELGG 257 Query: 300 NNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRV 359 +A + F DA+L V +A GQ C+ R+ H ++DEVV RL I+V Sbjct: 258 KSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAARAKSIKV 317 Query: 360 GNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLGH 419 G+P GPL + + LG V+ + EG ++V GG + G +VEPT+ + H Sbjct: 318 GDPSSRETSMGPLISAAQMKTVLGYVDAGRSEGASLVTGGGRIGERGFFVEPTVFANVEH 377 Query: 420 DASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCG 479 + I+ E F P+ V +F +E + N L++ +++ D+GR+ R D Sbjct: 378 EMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHR----VARDLR 433 Query: 480 IVNVNIPTSG-AEIGGAFGGEKHTGGGRESGSDAWKQY 516 V I T G ++ +GG +G GRE G A + + Sbjct: 434 AGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENF 471 Lambda K H 0.318 0.136 0.417 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: 657 Number of extensions: 33 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: 539 Length of database: 483 Length adjustment: 34 Effective length of query: 505 Effective length of database: 449 Effective search space: 226745 Effective search space used: 226745 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Sep 17 2021. 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