Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate PfGW456L13_5044 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= curated2:Q9AAL5 (472 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5044 Length = 481 Score = 221 bits (563), Expect = 4e-62 Identities = 150/443 (33%), Positives = 221/443 (49%), Gaps = 12/443 (2%) Query: 15 EAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVRARREEIATLIAR 74 +AI D+A D + AA +ARAAF W+ + + R + + ARREE+ TL+AR Sbjct: 32 DAIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARHDSLDKVGTEILARREELGTLLAR 91 Query: 75 ETGKPMWEALTEADSVAAKVAISIRAQDERAGERSEPMA--DATARLAHRPHGVLAVIGP 132 E GK + EA+ E A + + R P + GV+ +I P Sbjct: 92 EEGKTLPEAIGEVTR-AGNIFKFFAGECLRLSGDYLPSVRPGVNVEVTREALGVVGLITP 150 Query: 133 FNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIVIGGGEA 192 +NFP+ + I PAL GN VV KP++ P C + E+ AG P V +V+G G Sbjct: 151 WNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRV 210 Query: 193 -GEALVRHEALDGVLFTGGVQAGRAIHRALADAPHKILALELGGNAPLVVWDVADIEAAA 251 G+ALV +DG+ FTG V GR I + K+ LE+GG P ++ D AD++ A Sbjct: 211 VGDALVHSPKVDGISFTGSVGVGRQIAVSCVSRQAKV-QLEMGGKNPQIILDDADLKQAV 269 Query: 252 HLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPAPFMGPVI 311 L VQSA+ + GQRCT + R I+ G D +EA+ M + +G ++ +GPV+ Sbjct: 270 ELSVQSAFYSTGQRCTASSRFIVTAGIH-DQFVEAMAERMKSIKVGHALKAGTD-IGPVV 327 Query: 312 DAHAAAQVLAAQDRMTADGGRPLRLAAVR--EARSALLSPGLIELTDAPLR--DEEIFGP 367 Q + D ++G R + + + L+P L ++A +R EEIFGP Sbjct: 328 SQAQLEQDMKYIDIGQSEGARLVSGGGLVTCDTEGYFLAPTLFADSEASMRISQEEIFGP 387 Query: 368 LLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTTGASSA 427 + + R AD++AALA+AN T FGL+AG+ + F +AG+V N PT G Sbjct: 388 VANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYH 447 Query: 428 APFGG-VGGSGNHRPSAYYAADY 449 PFGG G S R YA ++ Sbjct: 448 VPFGGRKGSSYGSREQGRYAQEF 470 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: 514 Number of extensions: 24 Number of successful extensions: 5 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: 481 Length adjustment: 33 Effective length of query: 439 Effective length of database: 448 Effective search space: 196672 Effective search space used: 196672 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: 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