Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298 Length = 481 Score = 220 bits (561), Expect = 7e-62 Identities = 165/470 (35%), Positives = 228/470 (48%), Gaps = 21/470 (4%) Query: 5 FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 +I+G WV GA ++ + E A A A V A+ +AR AF AWS + AR Sbjct: 10 YINGQWVAGADYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPAWSTSGIQARHD 69 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 + + + ++ R+E L ++ RE GK L EA EV +G+ + Sbjct: 70 ALDKVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPSV 129 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 GV V + GVV + P+NFP +P I PAL GN VV KP+EL PG A A E Sbjct: 130 RPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALAE 189 Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I AG PAG NLV G + G L N ++DG+ FTGS G + R + + Sbjct: 190 IISRAGFPAGAFNLVMGSGRVVGDILVNSPKVDGISFTGSVGVGRQIAVNCVSR-QAKVQ 248 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 LEMGG NP ++ + D+ AV A+QSAF S GQRCT + R++V G D+FVA +A+ Sbjct: 249 LEMGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTAG-IHDKFVAAMAER 307 Query: 303 ASKITASVFDADPQPFMGAVISARAASRLV-------AAQARLVGLGASPIIEMKQRDPA 355 I +G V+S S+ + + ARLV G + + Sbjct: 308 MQSIKVG-HALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGGLVTCDTE----- 361 Query: 356 LGFVNAAIL--DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDE 413 G+ A L D + EE FGP+A +VR D + A+A ANDT FGLSAG+ Sbjct: 362 -GYFLAPTLFADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL 420 Query: 414 QAWHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462 + + F+R +AG+V N PT G PFGG G S R YA ++ Sbjct: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEF 470 Lambda K H 0.320 0.134 0.402 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: 488 Number of extensions: 19 Number of successful extensions: 4 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: 487 Length of database: 481 Length adjustment: 34 Effective length of query: 453 Effective length of database: 447 Effective search space: 202491 Effective search space used: 202491 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