Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::P25526 (482 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 224 bits (571), Expect = 1e-62 Identities = 149/462 (32%), Positives = 227/462 (49%), Gaps = 13/462 (2%) Query: 21 DANNGEAIDVTNPAN-GDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERATILRNW 79 D + I TNPA + + S+ + G E AI AA +A WR + +RA LR Sbjct: 520 DVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADRAAYLRRA 579 Query: 80 FNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGHQADKR 139 ++ + +L+ +E GK +A +++ F+E++A E R+ G + Sbjct: 580 ADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEH 639 Query: 140 LIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAELAIRA 199 + QP G+ A I PWNFP A+ A A+ G ++ KP+S + LAE+ A Sbjct: 640 NHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREA 699 Query: 200 GVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCAK------DIKKVS 253 G+P GVFN G + +G+ L +P + + FTGS E+G ++ E+ AK K+V Sbjct: 700 GLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVI 759 Query: 254 LELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAV 313 E+GG I+ DDADLD+AV L S F GQ C +R+ V D +YDRF E+L +A Sbjct: 760 AEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFIERLVKAA 819 Query: 314 SKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGGNFFQPTIL 373 S +HIG D +GP+ D V ++I A E+G RV+ G + TI+ Sbjct: 820 SSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEG-RVLLKRTDLPAEGCYVPLTIV 878 Query: 374 VDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEAL 433 D+ ++++EE FGP+ + R + ++ AN T F L ++R + + Sbjct: 879 GDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREF 938 Query: 434 EYGIVGINTGIISN--EVAPFGGIKASGLGREGSKYGIEDYL 473 G + +N G E PFGG SG+ GSK G DYL Sbjct: 939 RVGNLYLNKGSTGALVERQPFGGFAMSGV---GSKTGGPDYL 977 Lambda K H 0.318 0.135 0.395 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: 1062 Number of extensions: 68 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: 482 Length of database: 1006 Length adjustment: 39 Effective length of query: 443 Effective length of database: 967 Effective search space: 428381 Effective search space used: 428381 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: 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