Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 15420 b1300 gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent (NCBI)
Query= curated2:Q9AAL5 (472 letters) >FitnessBrowser__Keio:15420 Length = 495 Score = 202 bits (513), Expect = 3e-56 Identities = 152/446 (34%), Positives = 220/446 (49%), Gaps = 12/446 (2%) Query: 10 DPYTGEAIADFAVNDARSIDAACHSARAAF--AEWAMTPLAERRAIALRFAETVRARREE 67 DP T +A A + ID A +AR F +W+++ A+R+A+ + A+ + A EE Sbjct: 41 DPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEE 100 Query: 68 IATLIARETGKPMWEALTEADSVAAK-VAISIRAQDERAGERSEPMADATARLAHRPHGV 126 +A L +TGKP+ +L + AA+ + A D+ GE + + A + P GV Sbjct: 101 LALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGV 160 Query: 127 LAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIV 186 +A I P+NFP+ L + PAL AGN+V+ KPSEK+P + L + AGLPD VL +V Sbjct: 161 IAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVV 220 Query: 187 IG-GGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPHKILALELGG-NAPLVVWDV 244 G G EAG+AL RH +D + FTG + G+ + + D+ K + LE GG +A +V D Sbjct: 221 TGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADC 280 Query: 245 ADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPA 304 D++ AA + GQ C RL+L E D L L G P PA Sbjct: 281 PDLQQAASATAAGIFYNQGQVCIAGTRLLLEESI-ADEFLALLKQQAQNWQPGHPL-DPA 338 Query: 305 PFMGPVIDAHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIELTD--APLRDE 362 MG +ID A V + + G L L +A + P + D A L E Sbjct: 339 TTMGTLIDCAHADSVHSFIREGESKG--QLLLDGRNAGLAAAIGPTIFVDVDPNASLSRE 396 Query: 363 EIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTT 422 EIFGP+L V R + AL LAN +++GL A + + D + R ++AG V N Sbjct: 397 EIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYND 456 Query: 423 GASSAAPFGGVGGSGNHRPSAYYAAD 448 G PFGG SGN R + +A + Sbjct: 457 G-DMTVPFGGYKQSGNGRDKSLHALE 481 Lambda K H 0.320 0.135 0.400 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: 544 Number of extensions: 24 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: 472 Length of database: 495 Length adjustment: 34 Effective length of query: 438 Effective length of database: 461 Effective search space: 201918 Effective search space used: 201918 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 (21.8 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