Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_015886765.1 NGR_RS03130 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_000018545.1:WP_015886765.1 Length = 475 Score = 211 bits (537), Expect = 4e-59 Identities = 161/466 (34%), Positives = 233/466 (50%), Gaps = 33/466 (7%) Query: 3 ELFIDGAWVD-GAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDA 61 + +IDG WV+ +P T + + A SA D E+AVA+ARRAFA++S Sbjct: 6 KFYIDGEWVEPSVSKTLEVIDPSTEQPMGTIALGSAADAEKAVAAARRAFASYSQTSKQE 65 Query: 62 RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASM-AAKVDISITAYHERTGEK 120 R +++R +L R + L +I RE G PL AR E A + AA + +I ++ + Sbjct: 66 RVELLRRILTILKRRNDELGDIISREMGAPLAMARAEQAGIGAAHFEQAIKSFETFAFD- 124 Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 G + H P GVVA+ P+N+P + + AL G T+V KPSE+AP A Sbjct: 125 ---YMQGTTRIVHEPVGVVAMITPWNWPINQIACKVAAALATGCTMVLKPSEIAPFNAVL 181 Query: 181 TVEIWRDAGLPAGVLNLVQGEKDT-GVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 EI +AG+P GV NLVQG+ T G ALA+H +D + FTGS+ G + + P + Sbjct: 182 FAEIMDEAGVPKGVFNLVQGDGPTVGAALASHPDVDMVSFTGSTRAGIAVAQ--AAAPTV 239 Query: 240 V-LALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298 + E+GG +P ++ D AAV ++ F ++GQ CT R+LVP A Sbjct: 240 KRVHQELGGKSPNIILRSADFPAAVAAGVRRCFGNSGQTCTAPTRMLVP---------AE 290 Query: 299 LADVASKITASVFDA-------DPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQ 351 D A I A DA D + +G V SA ++ A R + GA + Sbjct: 291 RMDEAGAIAARQADALVVGPPSDSRTDLGPVASAAQFDKIQALIERGIAEGAELVAGGLG 350 Query: 352 RDPALG---FVNAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAG 407 R L +V + VTN + EE FGP+ I+ Y D+AIA ANDT +GL+A Sbjct: 351 RPSHLNAGYYVRPTVFARVTNQMSIAREEIFGPVLSIIGYDSEDEAIAVANDTPYGLAAY 410 Query: 408 LLADDEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHR 453 + D ++ +R+G V N ++G SAAPFGG +SGN R Sbjct: 411 IQGDPKET-RALAGKLRSGTVRLN--SSGWDSAAPFGGYKQSGNGR 453 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: 491 Number of extensions: 27 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: 475 Length adjustment: 34 Effective length of query: 453 Effective length of database: 441 Effective search space: 199773 Effective search space used: 199773 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 Apr 09 2024. 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