Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Ac3H11_612 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_612 Length = 483 Score = 216 bits (550), Expect = 1e-60 Identities = 158/463 (34%), Positives = 219/463 (47%), Gaps = 10/463 (2%) Query: 6 IDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCTI 65 I+G W G ++ T E V E A A + E AV +A A WS R + Sbjct: 14 INGRWEIGTTTGISTNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQRRADV 73 Query: 66 VKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPMA 125 + + L+ RK+ L ++ RE GK L E EVA GE A + Sbjct: 74 LDMIGSELLARKDELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELLASVR 133 Query: 126 DGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVEI 184 GV V + P GVV + P+NFP +P I PAL GNTVVFKP+EL P A EI Sbjct: 134 QGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAEI 193 Query: 185 WRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLAL 243 +GLPAG NL+ G ++ G L +H ++ L FTGS TG + + R + L Sbjct: 194 ISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQR-RAKVQL 252 Query: 244 EMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLAD-V 302 EMGG NPL+V D+D AV A+Q ++ S GQRCT + R++V D FVARL + + Sbjct: 253 EMGGKNPLIVLADADLDQAVDCALQGSYFSTGQRCTASSRLIV-EAEVHDAFVARLRNRL 311 Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPII--EMKQRDPALGFVN 360 AS + + MG V+ ++ + GA + E +R +++ Sbjct: 312 ASLKVGHALERGTE--MGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGHYMS 369 Query: 361 AAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHTFR 420 A+ + EE FGP+A ++R D D A+A ANDT FGL AG+ + F+ Sbjct: 370 PALFLARPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFK 429 Query: 421 RAIRAGIVNWNRPTNGASSAAPFGGAGRSG-NHRPSAYYAADY 462 R G+ N PT G PFGG S R YAA++ Sbjct: 430 RHAAVGMTMVNLPTAGVDFHVPFGGRKESSYGAREQGRYAAEF 472 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: 540 Number of extensions: 34 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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