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 YP_004144810.1 Mesci_5685 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000185905.1:YP_004144810.1 Length = 477 Score = 365 bits (937), Expect = e-105 Identities = 198/467 (42%), Positives = 280/467 (59%), Gaps = 4/467 (0%) Query: 10 QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69 QL I+G+W S T+ VVNPAT K VA A ++DLD ALA+A+ +AW PA + Sbjct: 8 QLFINGKWRAGGSRATLPVVNPATEKVFASVASATVSDLDEALASAERSRKAWSSRPAKD 67 Query: 70 RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129 R + AA ++ E+A A A+ ++ EQGK + EA E L A + +EW GR + Sbjct: 68 RGEILVAAARILAEKAGAAARDLSAEQGKTIAEATGEYLRAVETLEW---NGRHAE-ELS 123 Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189 P +G + VV E +G VAAFTPWN+P + RKL+ ALA GC ++K EETP+ Sbjct: 124 APIPVGPNRMVVPESLGVVAAFTPWNYPAVLIARKLAPALAAGCPVILKGAEETPSVAVH 183 Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249 ++ + AG+P GV+ LV+G P IS +L+ P+++ +TFTGST VGKQLA+LA +++R Sbjct: 184 IVESLRQAGIPDGVVNLVFGVPVHISRHLLSSPIVKVLTFTGSTEVGKQLATLAANNLQR 243 Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309 +ELGGH+PVIV EDAD+ A+ A KF AGQ C +P+R LV S +EF + Sbjct: 244 CILELGGHSPVIVCEDADLGKAIPAISEYKFECAGQSCNAPSRVLVARSRYEEFLSQMTD 303 Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369 A +K+G + T +G +AN RR+ AM + +A + GA IETGG R+ G ++ PT Sbjct: 304 AARKIKIGLPDDPSTDMGPMANTRRIEAMQRLTKDAVERGARIETGGSRLDRPGFYWPPT 363 Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429 ++ VP +A V + EPFGP+ I FD+L+EAI EAN +GLA Y FT + L Sbjct: 364 ILTGVPKEARVLHEEPFGPILTIAPFDELDEAIEEANATDYGLAAYFFTDAANAQRKLIN 423 Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 L G + +N + P+GGVK SGYG EGG + + + + K V Sbjct: 424 SLSAGAVSVNYLKGVSADAPYGGVKQSGYGYEGGEQGVRSFQILKMV 470 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: 584 Number of extensions: 23 Number of successful extensions: 2 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: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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