Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_085770261.1 B1812_RS02885 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= curated2:Q2G9T9 (471 letters) >NCBI__GCF_002117405.1:WP_085770261.1 Length = 1018 Score = 208 bits (530), Expect = 6e-58 Identities = 163/478 (34%), Positives = 223/478 (46%), Gaps = 32/478 (6%) Query: 9 HEPATGAEVWRGKVGDVEEV--------VARARRAWPAWAAQPLATRIELVRRFANEVRK 60 H P G +VGDV E +A A RA+ AW AQP TR +++ R A + Sbjct: 550 HSPFDGT-----RVGDVIEADAASLDVAMAAAHRAFSAWGAQPAETRAQILERAAALIES 604 Query: 61 DADNLATMISRETGKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAA---- 116 L ++ E GK L +A EV + R YA+ + + AL G Sbjct: 605 RRGRLIALLQSEGGKTLDDALAEVREAADYC----RYYANVARELMRERALPGPTGEENR 660 Query: 117 LRHKPHGVLAVLGPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGI 176 LRH GV + P+NFP + G I AL+AGNAV KP+E+TP G AG+ Sbjct: 661 LRHVGRGVFVCISPWNFPLAIFVGQIAAALVAGNAVAAKPAEQTPLIGFEAVALLREAGV 720 Query: 177 PAAVVQVLIGGPEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASNPGKIVAL--EMGGN 234 PA +Q L G G +LVAH+ GV+FTGS INR LA PG IV L E GG Sbjct: 721 PADALQFLPGDGAVGASLVAHELTAGVVFTGSVAVAQEINRALAKKPGPIVPLIAETGGI 780 Query: 235 NPIVVWDTPKIEDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVG 294 N ++V T E A + SAF SAGQRC+A R L ++ +FD + + A + +G Sbjct: 781 NAMIVDSTALFEHVADDVCASAFRSAGQRCSALRLLYLQEEIFDACLATIVGAAKELRLG 840 Query: 295 APFDDPAPFMGPVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAV 354 P DPA +GPVID L + + G + + F++P ++ +++ Sbjct: 841 DP-GDPATHIGPVIDRGAKAALDDYLARRRAEGS--VVYTGAAPGQGCFVAPHVVRLSSG 897 Query: 355 ADRPDVELFGPLLQVV--RVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGV 412 + + E+FGP+L V R DFD +AE +GL+ L R A AG Sbjct: 898 REL-NQEIFGPVLHVAPWRAGDFDSLVAEIMAANYGLTIGLHSRIEARAKRLAALAPAGN 956 Query: 413 VNWNRPTNGA-SSAAPFGGVGLSGNHRPSAYYAADYCAYPVASTEVDQPRASIGVGLR 469 + NR GA + PFGG LSG + ADY V V A++G LR Sbjct: 957 IYINRTMIGAVVGSQPFGGFNLSGTGPKAG--GADYLRRFVREITVTTNTAALGGDLR 1012 Lambda K H 0.319 0.135 0.403 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: 1125 Number of extensions: 55 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: 471 Length of database: 1018 Length adjustment: 39 Effective length of query: 432 Effective length of database: 979 Effective search space: 422928 Effective search space used: 422928 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 (21.7 bits) S2: 54 (25.4 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