Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate AO353_24855 AO353_24855 aldehyde dehydrogenase
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24855 Length = 471 Score = 204 bits (519), Expect = 5e-57 Identities = 154/459 (33%), Positives = 231/459 (50%), Gaps = 24/459 (5%) Query: 4 WIAGEWVQGQGEEFVS-LSPYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAERE 62 +I G W G+ ++P +EV V+ AVAAAR AF W + P + R Sbjct: 8 FIDGRWQTPSGQGIAEVINPATEEVAGSVPLGDERDVENAVAAARRAFGPWSRTPSSVRA 67 Query: 63 AIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEAAAMAGKIAISIRAYHDRTG--EAT 120 + A AE+++ ++++A +I E G P+ R+ + G I + Y + + Sbjct: 68 GYIRALAEQLRARADEMAALITAELGMPVQWCRS--VQVDGPIT-GLEQYVELASLMDEV 124 Query: 121 REAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTGELA 180 RE GN +V+R P+GV A P+N+P H G + PAL AG TVV KPS++TP L Sbjct: 125 REV-GNSLVIRE-PVGVCAFINPWNYPLHQLIGKLAPALAAGCTVVVKPSQETPLHAFLL 182 Query: 181 MKLWEEAGLPKGVINLVQG-AKETGIALADAKGIDGILFTGSANTGHILHRQFAGQPGKM 239 ++ E GLP GV NLV G + G ALA +D + FTGS G + Q A K Sbjct: 183 AQMIEAIGLPAGVFNLVSGPGSKVGEALAKHPDVDMVSFTGSTGAG-VRVAQAAAPSVKR 241 Query: 240 LALEMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALITKL 299 + LE+GG +P++I+++ DL A V +Q I++GQ CT R+ +P + + L Sbjct: 242 VCLELGGKSPLLIAED-ADLAAAVRYGVQDVMINSGQTCTALTRMLLPASRYAEVVELAL 300 Query: 300 VEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDAQANLQSLGGESLIEAKAGEA----A 355 E T ++RM P +P F+GP S A + + D Q G + +A Sbjct: 301 AE-TLSLRMGDPL-DPQSFLGPMCSAAQRRTVRDYIQVGQQEGARLVCGGDTAQAFERGY 358 Query: 356 FVSPGII-DVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSAGLVSTDDQEW 414 +VSP + DV N + EE FGP+L ++ Y +A+++AND+ FGLS+G+ + Sbjct: 359 YVSPTLFADVDNRMRIAQEEIFGPVLCLIPYTDEAQAIQIANDSPFGLSSGVWAGSPDRA 418 Query: 415 EYFVDHIRAGIVNRNRQLTGASGD--APFGGPGASGNLR 451 +RAG L GA+ + APFGG SGN R Sbjct: 419 LQLARQLRAG----QCFLNGAAFNYLAPFGGYKQSGNGR 453 Lambda K H 0.316 0.134 0.397 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: 568 Number of extensions: 36 Number of successful extensions: 6 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: 485 Length of database: 471 Length adjustment: 34 Effective length of query: 451 Effective length of database: 437 Effective search space: 197087 Effective search space used: 197087 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: 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