Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q9S795 (501 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 325 bits (832), Expect = 3e-93 Identities = 184/477 (38%), Positives = 265/477 (55%), Gaps = 10/477 (2%) Query: 11 FIDGEWREPILKKRIPIVNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGKDWAKAP 70 FI +W E KK + + NPAT EV+G +P ++ A++AA +L W Sbjct: 15 FIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPA-----WRSKT 69 Query: 71 GAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLAEGLDA 130 A R+ LR + E + DLA L + GKPL E+ ++ A FE++A+ A+ + Sbjct: 70 AAQRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESRGEIAYAASFFEWFAEEAKRIYG 129 Query: 131 KQKAPVSLPMESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILKPSELA 190 + + S + V+KQP+GVV ITPWN+P M K +LAAGCT ++KP+ Sbjct: 130 DI---IPQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATAT 186 Query: 191 SVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSKVMTAA 250 + L +A + +E G+PPGV NV+TG S G L ++P V K+ FTGS G K+M Sbjct: 187 PFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDC 246 Query: 251 AQLVKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHESIASEF 310 A +K VSMELGG +P IVFDD DLD A E AL + +GQ C +RL V + +F Sbjct: 247 AGTMKRVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQF 306 Query: 311 IEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGSRPEHLE 370 EKL + +K+ + +EEG GP++ E + + I+ A +GA +L GG R H Sbjct: 307 CEKLARAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR--HAL 364 Query: 371 KGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHYGLGAAVISNDT 430 G F PT++ DVT M + +EE+FGP + F SE E ++ AND+ YGL A + D Sbjct: 365 GGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDM 424 Query: 431 ERCDRISEAFEAGIVWINCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTL 487 R R+ E E G++ IN AP+GGVK SG GRE ++GLD+YL +K + + Sbjct: 425 ARTWRVGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481 Lambda K H 0.318 0.135 0.416 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: 584 Number of extensions: 19 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: 501 Length of database: 485 Length adjustment: 34 Effective length of query: 467 Effective length of database: 451 Effective search space: 210617 Effective search space used: 210617 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 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