Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 317 bits (813), Expect = 5e-91 Identities = 186/480 (38%), Positives = 267/480 (55%), Gaps = 10/480 (2%) Query: 30 QQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQL 89 + P + C FI ++W +A S+K NP+TGEV+ V ++ +A+ AA + Sbjct: 5 KDPGLLCQACFIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA 64 Query: 90 GSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYY 149 WR A+ R +L R DL+ ++ LA L T + GKP S ++ ++ Sbjct: 65 ---WRSKTAAQRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESR-GEIAYAASFFEWF 120 Query: 150 AGWADKYHGKTIP--IDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVV 207 A A + +G IP I + +PVGV I PWNFP M K G ALA G +V Sbjct: 121 AEEAKRIYGDIIPQTIASQRLVVIK-QPVGVVAAITPWNFPSAMITRKAGAALAAGCTMV 179 Query: 208 MKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG 267 +K A TP +AL +A L +EAG PPGV N+V G G + ++ V K+ FTGSTE+G Sbjct: 180 VKPATATPFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVG 239 Query: 268 R-VIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTF 326 + ++Q AG+ +KRV++ELGG +P I+ DAD+D AVE A + N GQ C +R + Sbjct: 240 KKLMQDCAGT--MKRVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLY 297 Query: 327 VQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLC 386 VQ +YD+F E+ + VGN + QGP +D + + +IN +GAK+L Sbjct: 298 VQAGVYDQFCEKLARAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLA 357 Query: 387 GGGIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAA 446 GG A G F PTV DV D M +AKEEIFGP I KF++ EVV +AN++ YGLAA Sbjct: 358 GGKRHALGGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAA 417 Query: 447 AVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506 FT+D+ + + + L+ G + +N + A +PFGG K SG+GRE +YGL Y E+K Sbjct: 418 YFFTRDMARTWRVGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIK 477 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: 591 Number of extensions: 28 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: 517 Length of database: 485 Length adjustment: 34 Effective length of query: 483 Effective length of database: 451 Effective search space: 217833 Effective search space used: 217833 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: 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