Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate SM_b21185 SM_b21185 succinate-semialdehyde dehydrogenase (NAD(P)+) protein
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__Smeli:SM_b21185 Length = 491 Score = 211 bits (536), Expect = 6e-59 Identities = 155/461 (33%), Positives = 233/461 (50%), Gaps = 26/461 (5%) Query: 14 AGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCTIVKRFAALL 73 AGPVF NP T E + DD A+ +A A W+ R I++R+ L+ Sbjct: 31 AGPVFDVSNPSTGELLATLPDMGIDDARTAIDAAALAQPLWAGKPAKDRSIILRRWHDLI 90 Query: 74 VERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK-RAPMADGVAVLR 132 VE + LA ++ E GKP+ EA+ EV A+ V+ GE AP D ++ Sbjct: 91 VEHADDLAAILTAEMGKPVGEAKGEVLHAASYVEWYAEEAKRVYGETFPAPANDRRMLVI 150 Query: 133 HRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVEIWRDAGLPA 192 +P GVV P+NFP + I PAL AG T+V KP+E P VA A + AG P Sbjct: 151 KQPVGVVGTITPWNFPASMVARKISPALAAGCTIVLKPAEQTPLVAGAMFVLAEKAGFPE 210 Query: 193 GVLNLVQGEKDT--GVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLALEMGGNNP 250 GVLNL+ + G L + ++ + FTGS++ G LL +Q + + V +LE+GGN P Sbjct: 211 GVLNLLYASEGAPIGRELCGNPKVRKISFTGSTEVGRLLMRQCSDQIKKV-SLELGGNAP 269 Query: 251 LVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVP---RGAFGDRFVARLADVASKIT 307 +V + DID AV A+Q+ F +AGQ C A RI V AF ++FV R+ ++ Sbjct: 270 FIVFDDADIDEAVDGAVQAKFRNAGQTCVSANRIYVQSAVHDAFAEKFVTRVREL----- 324 Query: 308 ASVFDA-DPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALG-----FVNA 361 +V D P +G +I A A ++ A A V GA +++ +G F Sbjct: 325 -TVGDGFAPDVAIGPMIDAHAIDKIEAHVADAVAKGA----QVRSGGSRIGTTGTFFEPT 379 Query: 362 AILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADD-EQAWHTFR 420 + +++ + EE FGP+A I+R+ + +A ANDT +GL+A A++ ++ WH Sbjct: 380 VLTGISHDMRIAQEETFGPIAPIIRFETAEQVVAEANDTIYGLAAYFYAENLKRVWHV-A 438 Query: 421 RAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461 A+ G+V N +S AAPFGG +SG R + + + Sbjct: 439 EALEYGMVGIN-TGRMSSEAAPFGGIKQSGIGREGSRHGLE 478 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: 526 Number of extensions: 24 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: 491 Length adjustment: 34 Effective length of query: 453 Effective length of database: 457 Effective search space: 207021 Effective search space used: 207021 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