Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate Pf6N2E2_1751 Aldehyde dehydrogenase A (EC 1.2.1.22) / Glycolaldehyde dehydrogenase (EC 1.2.1.21)
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1751 Length = 477 Score = 320 bits (820), Expect = 7e-92 Identities = 176/463 (38%), Positives = 269/463 (58%), Gaps = 4/463 (0%) Query: 12 QAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKE 71 Q Y+ A+V +D + ++V+NPA G+++G VP+ AE +AI AA +A AW A A E Sbjct: 7 QNYIANAFVASD--EHLEVHNPANGQLLGRVPQGSTAEVEQAIAAARQAQRAWAARPAIE 64 Query: 72 RANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTI 131 RA LR+ + E+ + LAR +T EQGK L A+ E+ + A +L++ E A+R+ G+ + Sbjct: 65 RAGYLRKIASKVREHGERLARTITAEQGKVLELARVEVNFTADYLDYMAEWARRLEGEVL 124 Query: 132 PGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALA 191 + + I ++++P+GV A I PWNFP +I RK PAL G T+V+KP+ +TP + Sbjct: 125 SSDRAGESIFLLRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPINCFE 184 Query: 192 LAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKK 251 A L +P GVF+VV G+ VG L+ +P + ++FTGS G ++MA A +I K Sbjct: 185 FARLVAETDLPAGVFNVVCGTGATVGHALSGHPGIDLISFTGSVGTGSRIMAAAAPNITK 244 Query: 252 VSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKA 311 ++LELGG AP IV DADLD A+ S+ N GQ C CA R+YV+ V DAF+D + A Sbjct: 245 LNLELGGKAPAIVLADADLDLAIRAITASRVINTGQVCNCAERVYVERKVADAFIDGIAA 304 Query: 312 AVAKLNIGNGL-EAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALG-GTFFE 369 ++A G+ L E G+ GPLI+ A+ KV + + A +GA++++GG LG G ++ Sbjct: 305 SMAATRYGDPLAEHGLDMGPLINRAALDKVAQMVRTASGQGAQIITGGAVADLGQGFHYQ 364 Query: 370 PTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRV 429 PT+L + + E FGP+ P+ D E IA++ND+E+GL S Y L+ + Sbjct: 365 PTVLAGCSAKMEIMRKEIFGPVLPIQIVDDLDEAIALANDSEYGLTSSIYTASLSAAMQA 424 Query: 430 AEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDY 472 L++G IN G + SG+G K+G+ +Y Sbjct: 425 TRLLDFGETYINRENFEAMQGFHAGTRKSGIGGADGKHGLYEY 467 Lambda K H 0.317 0.135 0.391 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: 521 Number of extensions: 17 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: 483 Length of database: 477 Length adjustment: 34 Effective length of query: 449 Effective length of database: 443 Effective search space: 198907 Effective search space used: 198907 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