Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 221 bits (562), Expect = 1e-61 Identities = 147/468 (31%), Positives = 223/468 (47%), Gaps = 15/468 (3%) Query: 14 YINGEWLDADNGQTIKVTNPAT-GEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKER 72 YI G D I TNPA EV+ ++ + G E AI AA KA WR + +R Sbjct: 515 YIGGR--DVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADR 572 Query: 73 SAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIP 132 +A LRR ++ + +L+ E GK +A ++ F+E++A E R+ Sbjct: 573 AAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRM 632 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192 G P + + QP G+ A I PWNFP A+ A A+ G ++ KP+S + L Sbjct: 633 GRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNL 692 Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK----- 247 E+ AG+P GV + G + +G L + + + FTGS E+G ++ E+ AK Sbjct: 693 AEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQ 752 Query: 248 -DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306 K+V E+GG I+ DDADLD+AV + S + GQ C +R+ V D +YD F Sbjct: 753 RQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFI 812 Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL-IEGNF 365 E+L A + + IG + GP+ D V ++I A +G +L L EG + Sbjct: 813 ERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCY 872 Query: 366 FEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVF 425 TI+ D+ +A+EE FGP+ + R E ++++N T F L ++R + Sbjct: 873 VPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLD 932 Query: 426 RVAEALEYGMVGINTGLISN--EVAPFGGIKASGLGREGSKYGIEDYL 471 + G + +N G E PFGG SG+ GSK G DYL Sbjct: 933 KARREFRVGNLYLNKGSTGALVERQPFGGFAMSGV---GSKTGGPDYL 977 Lambda K H 0.317 0.134 0.384 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: 1041 Number of extensions: 63 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: 480 Length of database: 1006 Length adjustment: 39 Effective length of query: 441 Effective length of database: 967 Effective search space: 426447 Effective search space used: 426447 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 (21.6 bits) S2: 54 (25.4 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