Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 155 bits (391), Expect = 4e-42 Identities = 138/467 (29%), Positives = 219/467 (46%), Gaps = 32/467 (6%) Query: 4 HYIAGQWLAG-QGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQR 62 ++I G+++ GE + + PV V A ++ A+ AA +AFPAW+R +R Sbjct: 24 NFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATER 83 Query: 63 IELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTG---E 119 +L + A ++++ + LA V + GKP+ E+ +A+ V FR G Sbjct: 84 SNILLKIADRIENKLEYLAAVETIDNGKPVRETINA------DLALVVDHFRYFAGVIRA 137 Query: 120 KSGPLAD----ATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTP 175 + G +A+ +V +P G+V P+NFP + + PAL AG C + KP+E TP Sbjct: 138 EEGSIAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTP 197 Query: 176 KVAELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFG 234 + + L I LPAGVLN+V G G E G LA LD + FTG + TG L+ Q+ Sbjct: 198 -ASIMILMEVIGDLLPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLI-MQYA 255 Query: 235 GQPQKILALEMGGNNPLV----VEEVAD--LDAAVYTIIQSAFISAGQRCTCARRLLVPQ 288 + + +E+GG +P V V + D LD + + A ++ G+ CTC R+LV + Sbjct: 256 SENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFA-LNQGEVCTCPSRILVHE 314 Query: 289 GAWGDALLARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLA 348 + DA + +++A + +++G MGA S E +L + +GA+ L Sbjct: 315 KIY-DAFMEKVIARAEAIQMGH-PLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTG 372 Query: 349 -----MTQPIDGAALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYG 403 + ++ + P +L EE FGP+ V + D AI +N T YG Sbjct: 373 GEVAKLNSGLENGYYVKPTLLKGHNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYG 432 Query: 404 LAAGLLSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASG 450 L AG+ + Q +AG V W + APFGG SG Sbjct: 433 LGAGVWTRDAHEAYQVPRAIKAGRV-WVNCYHAYPAHAPFGGYKKSG 478 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: 557 Number of extensions: 36 Number of successful extensions: 6 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: 509 Length adjustment: 34 Effective length of query: 453 Effective length of database: 475 Effective search space: 215175 Effective search space used: 215175 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