Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= SwissProt::Q8ZPV0 (492 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 200 bits (509), Expect = 8e-56 Identities = 154/473 (32%), Positives = 233/473 (49%), Gaps = 26/473 (5%) Query: 4 WINGDWI-TGQGERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPR--WARQPFAA 60 +I+G W G NP + + L + A V A AAR AF W+ P +A Sbjct: 24 YIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAAARKAFQSGVWSDTPRSA 83 Query: 61 RQAIVEKFAALLEAHKAELTEVIARETGKPRWEA-------ATEVTAMINKIAISIKAYH 113 R+A + + + L+E H+ EL + + GKP E A A + I Sbjct: 84 RKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAGRTYAWYAEAIDKIYDEI 143 Query: 114 ARTGAQKSELVDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELT 173 A TG AT+ P GV+A P+N+P + + + PAL AGN+++ KP+E + Sbjct: 144 APTGPGV------LATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGNSVVLKPAEQS 197 Query: 174 PWTGETVIKLWERAGLPAGVLNLVQG-GRETGQALSSLDDLDGLLFTGSASTGYQLHRQL 232 P T + +L E AG+PAGV N+V G G GQAL D+D + FTGS +TG + + Sbjct: 198 PLTALRLAELAEEAGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGSTATGKRF-MEY 256 Query: 233 SGQPE-KILALEMGGNNP-LIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQGAQ 290 SGQ K + LE GG +P ++ +D ++D A F G+ C RL V+ G Sbjct: 257 SGQSNLKRVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGSRLYVQSGIY 316 Query: 291 GDAFLARLVDVAGRLQPGRWDDDPQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRK 350 DAF+ +L A R+QPG DP +G ++ Q VM + E G R ++ Sbjct: 317 -DAFMEKLEAHAARMQPGD-PLDPATAMGAIVDGAQLQRVMSYVKSGEDEGARLRAGGKR 374 Query: 351 --VKEGTSLLTPGIIEL-TGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGL 407 G + P I E T + EE+FGP+L V R+ +EAIR+AN++ +GL GL Sbjct: 375 AHTDSGGFYMQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSPYGLGSGL 434 Query: 408 VSTDRAQFEQLLLEARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAAD 460 +++ ++ ++ + +AG+V W + T PFGGV SG+ R + +A D Sbjct: 435 WTSNLSRAHRVSRKLQAGLV-WVNCYMDSDVTVPFGGVKQSGSGRDKSLHALD 486 Lambda K H 0.319 0.134 0.411 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: 598 Number of extensions: 40 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: 492 Length of database: 499 Length adjustment: 34 Effective length of query: 458 Effective length of database: 465 Effective search space: 212970 Effective search space used: 212970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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