Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate SMa0260 SMa0260 GabD3 succinate-semialdehyde dehdyrogenase
Query= curated2:Q9AAL5 (472 letters) >FitnessBrowser__Smeli:SMa0260 Length = 487 Score = 190 bits (483), Expect = 8e-53 Identities = 158/477 (33%), Positives = 219/477 (45%), Gaps = 46/477 (9%) Query: 2 SASRLISRDPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETV 61 S S + DP TG +A+ A A +A AA A W TP +R I R+ + + Sbjct: 28 SGSGITVLDPSTGNLLAEVADASIEDAQRAVDAADAAAAGWRATPARQRSEILRRWYQLM 87 Query: 62 RARREEIATLIARETGKPMWEALTEADSVAAKVAISIRAQDERA----GE-RSEPMADAT 116 EE+ATLIA E GK AL +A A A R E A GE R P Sbjct: 88 TQHAEELATLIALENGK----ALADARGEVAYAAEFFRWYAEEATRIPGEFRHTPSGSHN 143 Query: 117 ARLAHRPHGVLAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAA 176 + H P G+ +I P+NFP +A I PAL AG V+ KP+ +TP M L A Sbjct: 144 ILVDHEPIGIAVLITPWNFPAAMATRKIGPALAAGCTVILKPASETPLTAYAMARLGEEA 203 Query: 177 GLPDHVLTIVIGGGEAG--EALVRHEALDGVLFTGGVQAGRAIHRALADAPHKIL--ALE 232 G+P V+ ++ G A++ + + FTG GR + LA+A ++ ++E Sbjct: 204 GVPPGVVNVLTTSNPGGITNAMLADPRVRKLSFTGSTGVGRVL---LAEAAKSVVSCSME 260 Query: 233 LGGNAPLVVWDVADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMD 292 LGGNAP +V+D AD+E A + + AG+ CT A R + G DA + LT M Sbjct: 261 LGGNAPFIVFDDADLEVALDGAMIAKMRNAGEACTAANRFYVQAGIH-DAFVAGLTARMK 319 Query: 293 RLVIGGPFQSPAPFMGPVIDAHA-------AAQVLAAQDRMTADGGRPLRLAAVREARSA 345 L + GP P GP+I +A ++ LAA R T GG+PL Sbjct: 320 SLKL-GPGYDPETQCGPMITQNAVRKIDRLVSEALAAGARATT-GGKPL------TENGY 371 Query: 346 LLSPGLIE--LTDAPLRDEEIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALY 403 P ++E +A + EEIFGP+ V + D A+ LAN T +GLAA + S D Sbjct: 372 FYPPTVLENVPVNASIAREEIFGPVAPVYKFESDDEAIRLANNTEYGLAAYIYSRDLKRA 431 Query: 404 RRFWTSVRAGIVNWNRPTTGASSAAPFGGVGGSGNHRPSA-----------YYAADY 449 + + G++ NR + AAPFGGV SG R Y+A DY Sbjct: 432 MKVGKRIETGMLGINRGLM-SDPAAPFGGVKQSGLGREGGVTGILEFMEPKYFAVDY 487 Lambda K H 0.320 0.135 0.400 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: 603 Number of extensions: 27 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: 472 Length of database: 487 Length adjustment: 34 Effective length of query: 438 Effective length of database: 453 Effective search space: 198414 Effective search space used: 198414 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: 51 (24.3 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