Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate SM_b20891 SM_b20891 dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__Smeli:SM_b20891 Length = 477 Score = 238 bits (608), Expect = 3e-67 Identities = 172/466 (36%), Positives = 236/466 (50%), Gaps = 16/466 (3%) Query: 6 IDGAWVDGAGPVFASRNPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 I G WV G G A+ NP T++ V E A ASA+D + A+A+A+ AF AWS + R Sbjct: 8 IAGEWVGGDG--VANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHA 65 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 I+K+ A ++ RK+ L ++ RE GK L E E + GE + Sbjct: 66 ILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSV 125 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 G+ V + P GVV + P+NFP +P + PAL GNT+VFKP+EL PG + A V+ Sbjct: 126 RPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVD 185 Query: 184 IWRDAGLPAGVLNLVQGEKD-TGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I AGLP GVLNLV G+ G A+ + + + FTGS+ TG + Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRV-AVASVEHNRKYQ 244 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 LEMGG NP VV + D+ AV A+ SAF S GQRCT + RI+V G DRFVA + + Sbjct: 245 LEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEG-IHDRFVAAMGE- 302 Query: 303 ASKITASVFD--ADPQPFMGAVISARAASRLV--AAQARLVGLGASPIIEMKQRD-PALG 357 +I V D P +G V+ ++ A + G + E+ RD P Sbjct: 303 --RIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFY 360 Query: 358 FVNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWH 417 A + TN + EE FGP+A ++R D D+A+A ANDT FGLS+G+ + Sbjct: 361 LQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHAT 420 Query: 418 TFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSG-NHRPSAYYAADY 462 F+R AG+V N PT G PFGG S R YAA++ Sbjct: 421 HFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEF 466 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: 527 Number of extensions: 22 Number of successful extensions: 3 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: 477 Length adjustment: 34 Effective length of query: 453 Effective length of database: 443 Effective search space: 200679 Effective search space used: 200679 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