Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 202865 SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__MR1:202865 Length = 1059 Score = 191 bits (486), Expect = 9e-53 Identities = 141/448 (31%), Positives = 222/448 (49%), Gaps = 23/448 (5%) Query: 61 TGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLA 120 T + + QVA DK +++AV +A AAF W R R L +LADL+E +R L Sbjct: 587 TTQTVGQVAFADKAAIEQAVSSAHAAF---GSWTRTPVEVRASALQKLADLLEENREELI 643 Query: 121 ALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFS----YTRHEPV 176 AL T + GK + + ++ + RYYA A K K + G + + V Sbjct: 644 ALCTREAGKS-IQDGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGV 702 Query: 177 GVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVN 236 VC I PWNFPL + ++ ALA GN VV K AEQT + L +AG P V+ Sbjct: 703 FVC--ISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQ 760 Query: 237 IVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQ--VAAGSSNLKRVTLELGGKSPNII 294 +PG G T G A+ + E + V FTGST ++I +A + + E GG++ ++ Sbjct: 761 YLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVV 820 Query: 295 MSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDS 354 S + + V + F + GQ C A F+QEDI D ++ V+GNP Sbjct: 821 DSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSI 880 Query: 355 KTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAA--DRGYFIQPTVFGDVQDGMTI 412 KT+ GP +D T + +I+ KQ G KL+ + A + G+F+ PT D + + Sbjct: 881 KTDVGPVIDATAKANLDAHIDHIKQVG-KLIKQMSLPAGTENGHFVAPTAV--EIDSIKV 937 Query: 413 AKEEIFGPVMQILKFKTIE--EVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWV 470 ++E FGP++ ++++K E V+ N++ +GL + +++ A ++ + G V++ Sbjct: 938 LEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYI 997 Query: 471 NCYD---VFGAQSPFGGYKMSGSGRELG 495 N V G Q PFGG +SG+G + G Sbjct: 998 NRNQIGAVVGVQ-PFGGQGLSGTGPKAG 1024 Lambda K H 0.319 0.136 0.409 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: 1121 Number of extensions: 55 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: 517 Length of database: 1059 Length adjustment: 40 Effective length of query: 477 Effective length of database: 1019 Effective search space: 486063 Effective search space used: 486063 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 (21.8 bits) S2: 55 (25.8 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