Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_000691145.1:WP_019744147.1 Length = 486 Score = 188 bits (477), Expect = 4e-52 Identities = 141/447 (31%), Positives = 213/447 (47%), Gaps = 9/447 (2%) Query: 5 FIDGAWVDG-AGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63 +I G WVD A NP T E + E ++ DVE AV +A+ AF WS + R Sbjct: 12 YIGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSKTAVPRRA 71 Query: 64 TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAP 123 I+ ++ LLVE+ + LA ++ E GK + EA+ EV V+ + A G++ Sbjct: 72 RILFKYQQLLVEKWDELAELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLMMGKQLPD 131 Query: 124 MADGVAVLRHR-PHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATV 182 +A G+ +R P GV+ P+NFP +P A+ GNT V KPSE P +A Sbjct: 132 IATGLESGMYRYPIGVIGGITPFNFPMMVPCWMFPLAIACGNTFVLKPSERTPILAARLA 191 Query: 183 EIWRDAGLPAGVLNLVQGEKDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 E++ +AGLP GVLN+V G D L H ++ + F GS ++K+ + V A Sbjct: 192 ELFEEAGLPKGVLNIVNGAHDVVNGLLEHEKVKAISFVGSQPVAEYVYKKGTAHGKRVQA 251 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 L G N +V + D+++A I +AF SAG+RC A + V D + +L D Sbjct: 252 L-AGAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDV-ADDLIQQLVDE 309 Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALG---FV 359 ++++ + F+G VI R + + GAS I + +Q + G FV Sbjct: 310 SNQLVIG-NGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQDNETNGEGYFV 368 Query: 360 NAAILD-VTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHT 418 I D VTN ++ +E F P+ IVR + L +AI +N + F A L D + Sbjct: 369 GPTIFDHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGACLYTDSASSIRE 428 Query: 419 FRRAIRAGIVNWNRPTNGASSAAPFGG 445 FR I AG++ N + PF G Sbjct: 429 FRENIEAGMLGINIGVPAPMAFFPFSG 455 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: 439 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: 486 Length adjustment: 34 Effective length of query: 453 Effective length of database: 452 Effective search space: 204756 Effective search space used: 204756 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 24 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