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 Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 259 bits (663), Expect = 1e-73 Identities = 158/473 (33%), Positives = 244/473 (51%), Gaps = 9/473 (1%) Query: 7 TDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVP 66 T +L++DG+ A +T V++PATG+P A ADLD A+AAA+ F W P Sbjct: 2 TGVRLIVDGK--PLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATP 59 Query: 67 AHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWF-ADEGRRVY 125 +RAA + A + D +A+L++ EQGKP+ A E++ A + W A G R Sbjct: 60 IEDRAAAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGA---LAWARATAGLRPA 116 Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185 ++ + + V ++P+G VA+ +PWNFPV + + L G + ++K TP Sbjct: 117 VDVLKDDD-SVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPL 175 Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245 + ++ +A +P GV+ V G+ EI + HP I K+ FTGSTP G+ + + Sbjct: 176 AALRMVE-IANAHLPPGVLNSVTGE-VEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAA 233 Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305 ++KR T+ELGG+ IV DADV F N+GQ+C + R VH SI D Sbjct: 234 NLKRLTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAE 293 Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNF 365 L + A VG G + + G + N ++ + ++ D+AR G GGE +G F Sbjct: 294 KLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYF 353 Query: 366 FAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVH 425 F +V+ +V + + E FGP+ + + E+A+A AN GL G ++ A Sbjct: 354 FPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAAL 413 Query: 426 LLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 QRLE G +W+N A+ P++PFGG K SG G+E G LE Y+ ++V V Sbjct: 414 AFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRV 466 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: 592 Number of extensions: 30 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 448 Effective length of database: 436 Effective search space: 195328 Effective search space used: 195328 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 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