Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate WP_047006047.1 AAW01_RS04300 aldehyde dehydrogenase family protein
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_001010925.1:WP_047006047.1 Length = 479 Score = 233 bits (593), Expect = 1e-65 Identities = 147/458 (32%), Positives = 232/458 (50%), Gaps = 11/458 (2%) Query: 26 IDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATMRKAAALVRERA 85 ++V++ TG+ RVA A +D+A+A A + ++ ++ER A + + RER Sbjct: 25 LEVIDKYTGEVAFRVAQADPEIIDKAIAGAVAATGPMARLASYERKAVLEHCVSRFRERF 84 Query: 86 DAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP----PRNLGAQQTVV 141 D +A + E GKP+ ++ EV D A+E R+YG ++P R G Q Sbjct: 85 DELAYALCVEAGKPIGDSEGEVTRLIDTFVIAAEESTRMYGEVMPLDISERAKGYQSIWK 144 Query: 142 KEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPA 201 + PVGP + +P+NFP+N K++ A+A GC F++K +TP + + +P Sbjct: 145 RYPVGPCSFISPFNFPLNLAAHKIAPAIAVGCPFVMKPASKTPLGAIIIGEILAETDLPE 204 Query: 202 GVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVI 261 G ++ + + ++ ++FTGS VG L + +G K+ +ELGG+A VI Sbjct: 205 GAFSILPAS-RDGADLFTEDERLKLLSFTGSPAVGWALKAKSG--KKKVVLELGGNAAVI 261 Query: 262 VAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGLE 321 V DAD+ A++ F +GQ CI R L+H + D F LV+ + LK G+ + Sbjct: 262 VDRDADLEDALERIVFGAFYQSGQSCIGVQRILIHEEVYDRFKEMLVEKTKTLKAGDPKD 321 Query: 322 EGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVF 381 T +G + + + ID A GA++ GG G +GN T++ V A V Sbjct: 322 RDTFIGPMIDEGEAQRLKGWIDEAVGHGATLLCGG---GCKGNMLEATLLEGVDKHAKVL 378 Query: 382 NNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQ- 440 N E FGP+A ++ F ++EA+ E NR FGL FTR + RLEVG + IN Sbjct: 379 NEEAFGPLAILQPFATMDEALEEVNRSEFGLQAGIFTRDLFAMFDAWDRLEVGGIVINDV 438 Query: 441 PATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 P+ MP+GGVKDSG G EG A+E +++ + Sbjct: 439 PSYRVDNMPYGGVKDSGLGREGIRFAMEDMTEIRNLVI 476 Lambda K H 0.318 0.134 0.393 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: 575 Number of extensions: 32 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: 481 Length of database: 479 Length adjustment: 34 Effective length of query: 447 Effective length of database: 445 Effective search space: 198915 Effective search space used: 198915 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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