Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Pf1N1B4_3024 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= SwissProt::Q8ZPV0 (492 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3024 Length = 474 Score = 194 bits (494), Expect = 4e-54 Identities = 155/469 (33%), Positives = 227/469 (48%), Gaps = 22/469 (4%) Query: 3 LWINGDWITGQGERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62 L ING + G G + NP +L + N+A+ AQV A +AA AF W++ R Sbjct: 5 LLINGQLVNGDGPAQAVFNPALGRVLVEINEASEAQVDAAVRAADNAFQAWSQTTPKERS 64 Query: 63 AIVEKFAALLEAHKAELTEVIARETGKPRWEAAT-EVTAMINKIAISIKAYHARTGAQKS 121 ++ K A ++EAH EL ++ + GKP A E+ A+ + A +GA Sbjct: 65 LLLLKLADIIEAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGANRCMSGALGG 124 Query: 122 ELVDG-AATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETV 180 E + G + +R P GV+A P+N+P + I PAL AGNT++ KPSE TP T Sbjct: 125 EYLPGHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPL---TA 181 Query: 181 IKLWERAG--LPAGVLNLVQG-GRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPE 237 ++L E A PAGVLNLV G G G AL + + + TGS +TG + +G + Sbjct: 182 LRLAELASDIFPAGVLNLVYGRGSAVGTALVNHPKVRMVSLTGSIATGSNIISSTAGNVK 241 Query: 238 KILALEMGGNNPLIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLAR 297 + L +E+GG P+II D A+IDAAV F AGQ CT A R+ + G D F+ + Sbjct: 242 R-LHMELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIY-DQFVEK 299 Query: 298 LVDVAGRLQPGRWDDDPQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTSL 357 L ++ G DDP +G LISAQ V + A L+ K EG Sbjct: 300 LGAAVSSIKYG-LQDDPSTELGPLISAQHRDRVTALVERAMAQPHIRLITGGKAVEGNGF 358 Query: 358 LTPGIIELTGVADVPDE------EVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTD 411 E T +ADV + EVFGP+++V R+ +A+ AN++ +GL+ + +TD Sbjct: 359 ----FFEPTVLADVQQDDEIVRREVFGPVVSVTRFTDEAQALAWANDSDYGLASSVWTTD 414 Query: 412 RAQFEQLLLEARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAAD 460 + +L + G W S P GG SG + + Y + Sbjct: 415 VGRAHRLSARLQYG-CTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLE 462 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: 590 Number of extensions: 25 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: 474 Length adjustment: 34 Effective length of query: 458 Effective length of database: 440 Effective search space: 201520 Effective search space used: 201520 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