Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate HSERO_RS11260 HSERO_RS11260 aldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__HerbieS:HSERO_RS11260 Length = 477 Score = 197 bits (501), Expect = 7e-55 Identities = 154/469 (32%), Positives = 226/469 (48%), Gaps = 17/469 (3%) Query: 1 MSTHYIAGQWLAG-QGETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFP-AWARR 57 M H+IA +W+A GE++ LDP GQ RG +AT +D AV AAR A+ AW R Sbjct: 1 MKQHFIANRWVAPTSGESIPVLDPSDGQPFDAIARG-NATDIDQAVRAARLAYEGAWGRL 59 Query: 58 PLEQRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERT 117 +R LL + A L+ +ELA++ G + GKP+ ++ + ++V A + Sbjct: 60 SAAERSRLLMKLAYKLQDHQEELAQLEGRDCGKPMKQARADAAAIVRYFEFYAGAADKLH 119 Query: 118 GEKSGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSE----L 173 G+ A T + +PHGV P+N+P + + AL AGN V KP+E Sbjct: 120 GDTIPYQAGYTVLTLREPHGVTGHIVPWNYPMQIFGRCVGGALAAGNTCVVKPAEDACLS 179 Query: 174 TPKVAELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQ 232 +VAEL + G P G LN+V G G E G L H ++ + FTGS G L+ + Sbjct: 180 ILRVAELA----AEVGFPEGALNIVTGYGHEAGDLLVKHPDVNHISFTGSPNVGKLV-VR 234 Query: 233 FGGQPQKILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWG 292 + + LE+GG +P +V E AD++A + ++ + +AGQ C+ RLLV +GA+ Sbjct: 235 AAAEHHTPVTLELGGKSPQIVFEDADMEAMLPVVVNAIVQNAGQTCSAGSRLLVQRGAY- 293 Query: 293 DALLARLVAVSATLRVG--RFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMT 350 + +L RL + + L+VG + D P + A L AQ I AQ +A Sbjct: 294 EQVLERLSGLFSQLQVGSSQMDLDCGPLIRKTQQERVAGFLSDAQRDGIALAAQGKIAAG 353 Query: 351 QPIDGAALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLS 410 P G + DV EE FGP+L + + D A AI AN T YGL A + + Sbjct: 354 VPTGGFYQAPALLRDVPPRHRLAQEEVFGPVLAAMPFEDEAHAIALANGTDYGLVASVWT 413 Query: 411 DSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459 R + R+G V N G PFGG+ ASG+ R + A Sbjct: 414 RDGGRQMRLARAIRSGQVFINNYGAGGGVELPFGGVKASGHGREKGFEA 462 Lambda K H 0.318 0.134 0.396 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: 552 Number of extensions: 39 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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