Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__psRCH2:GFF882 Length = 499 Score = 213 bits (543), Expect = 1e-59 Identities = 144/478 (30%), Positives = 241/478 (50%), Gaps = 27/478 (5%) Query: 63 GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122 GE + PAN + + + A+ AD + V+ A+ A+ W +R + +I D L Sbjct: 31 GETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFMTWRTTSPAERANALLKIADLLE 90 Query: 123 EKIQVLGSLVSLEMGKILVEGVG-EVQEYVDICDYAVGLSRMIGGP--ILPSERSGHALI 179 L +L++GK + E ++ +D Y G+ R +L + AL Sbjct: 91 ADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDEAVMLDEQTLSIALS 150 Query: 180 EQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLE 239 E P+G+VG + +NFP+ + W A A+ GN + K + T + + + KI AKVL Sbjct: 151 E---PLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTILELAKIFAKVL- 206 Query: 240 DNKLPGAICSLTCG-GADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELG 298 P + ++ G G +G A+ + L+FTGST+VG+ V ++ + LELG Sbjct: 207 ----PAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVANAAAKKIIPATLELG 262 Query: 299 GNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIR 358 G +A I F DA+ V A+ A + GQ C + RLF+HESI++ + LK + +R Sbjct: 263 GKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAELKHKFEAVR 322 Query: 359 VGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMD----RPGNYVEPTIV 414 VG+P +P+ + G +K + LG V+ AK+EG V+ GG + G +++PTI+ Sbjct: 323 VGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGGRLTGANYDAGFFIQPTIL 382 Query: 415 TGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPK 474 G+ +D +A+ E F P+L V FK+E EV A N+ + GL+ +++T+D+ R R + Sbjct: 383 VGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINRALR--VAR 440 Query: 475 GSDCGIVNVN----IPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSK 528 + G + VN IP FGG K +G GRE+ + Y ++ ++ ++ Sbjct: 441 AVETGRMWVNTYHEIPAH-----APFGGYKKSGLGRETHKSMLEAYSQKKNIYVSLNE 493 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: 666 Number of extensions: 36 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: 539 Length of database: 499 Length adjustment: 35 Effective length of query: 504 Effective length of database: 464 Effective search space: 233856 Effective search space used: 233856 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