Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate RR42_RS24555 RR42_RS24555 succinate-semialdehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Cup4G11:RR42_RS24555 Length = 494 Score = 221 bits (563), Expect = 5e-62 Identities = 140/459 (30%), Positives = 225/459 (49%), Gaps = 10/459 (2%) Query: 60 GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGD 119 GGR +T PA E +ARV S A+ E + + +A +W + +R +++R D Sbjct: 36 GGRSFAVTN--PATGEILARVASLSGAEVESAITASAQAQAVWQRRSSHERAKLLRAWFD 93 Query: 120 ALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALI 179 + L +++ E GK L E GE+ ++ ++ I G + P ++ ++ Sbjct: 94 LMIANADDLALIMTSEQGKPLAEARGEILYAASFVEWFAEEAKRIYGDVAPHPQTDKRIL 153 Query: 180 EQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLE 239 PVG+ IT +NFP A+ A A+ G + + A T L ++A +A + E Sbjct: 154 VIRQPVGVCAAITPWNFPAAMITRKVAPALAAGCSIIVRPADLTPLTALA----LAVLAE 209 Query: 240 DNKLPGAICSLTCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELG 298 +P + + CG + +IG + V LSFTGST+VG+ + R LELG Sbjct: 210 RAGIPAGVLQMVCGPSREIGAVLTASPVVRKLSFTGSTEVGRVLMSQSSPTIKRLSLELG 269 Query: 299 GNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIR 358 GN I F+DADL + A+ + +GQ C A R + + I+D V L + A+++ Sbjct: 270 GNAPFIVFDDADLDAAIEGAMASKYRNSGQTCVCANRFLVQDGIYDRFVEALVRRVAELK 329 Query: 359 VGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLG 418 VGN +P V GPL K A +++A +G VV GGK G + EPT++ G Sbjct: 330 VGNGVEPGVQQGPLIQKSACEHLQAMIDDAVGKGAKVVVGGKGHALGGTFFEPTVIAGAT 389 Query: 419 HDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDC 478 D +A E F P+ VF+F++E E A N+ + GL++ ++T+D RI W + + Sbjct: 390 PDMRVAREELFGPVAPVFRFRDEAEAIALANDTEYGLAAYLYTRDNARI--WRVGEALEY 447 Query: 479 GIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 G+V +N E+ FGG K +G GRE +Y+ Sbjct: 448 GMVGLNTGLISNEV-APFGGVKQSGLGREGSRYGIDEYL 485 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: 678 Number of extensions: 26 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: 494 Length adjustment: 35 Effective length of query: 504 Effective length of database: 459 Effective search space: 231336 Effective search space used: 231336 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