Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_054255670.1 BN2503_RS05615 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= curated2:Q2G9T9 (471 letters) >NCBI__GCF_001298675.1:WP_054255670.1 Length = 1335 Score = 186 bits (473), Expect = 3e-51 Identities = 140/430 (32%), Positives = 216/430 (50%), Gaps = 26/430 (6%) Query: 17 VWRGKVGDVEEVVARARRAWPAWAAQPLATRIELVRRFANEVRKDADNLATMISRETGKP 76 V+ DV+ RA +A P WA P ATR + ++R A+ + + + L +I RE GK Sbjct: 685 VYEAAAHDVQAACERAAQAAPIWAGTPPATRADALQRAADLLEQRSQPLMGLIMREAGKT 744 Query: 77 LWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAALRHKPHGVLAVLGPYNFPAH 136 L A E+ V+ +R Y + + + D+A Q +P GV+ + P+NFP Sbjct: 745 LPNAVAEIREAVD----FLRYYGAQVATQ-FDNAAQ-------RPLGVVLAISPWNFPLA 792 Query: 137 LPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGIPAAVVQVLIG-GPEEGQALV 195 + G + AL AGN V+ KP+E+TP T + H AG+P +Q++ G G G ALV Sbjct: 793 IFCGQVAAALAAGNTVLAKPAEQTPLTAAAMVALLHEAGVPRDALQLVPGQGESVGAALV 852 Query: 196 AHDGIDGVLFTGSAHAGIAINRKLA---SNPGKIVAL--EMGGNNPIVVWDTPKIEDAAT 250 AH + GV+FTGS I R+L+ S G+ + L E GG N +VV + E Sbjct: 853 AHPQVAGVMFTGSTEVARLIARQLSTRLSPTGQAIPLVAETGGQNAMVVDSSALAEQVVA 912 Query: 251 LIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGAPFDDPAPFMGPVIDN 310 ++ SAF SAGQRC+A R L ++ + D + ++ +G P D +GPVID Sbjct: 913 DVLASAFDSAGQRCSALRLLCLQDDVADRTLTMLRDALQEWTLGNP-DRLHTDVGPVID- 970 Query: 311 RTADGLTESFVYLLSSGGRPIKHMVRLQE--DRPFLSPAIIDVTAVADRPDVELFGPLLQ 368 A E+ + ++ G+ + + R + F++PAII++ + + R E+FGP+L Sbjct: 971 AEARAQIEAHIARMADAGQTVTRVERTDGALNGHFVAPAIIEIDSTS-RLTREVFGPVLH 1029 Query: 369 VVRV--DDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVVNWNRPTNGA-SSA 425 V+R + D + N T +GL+ + + I AG + NR GA Sbjct: 1030 VIRYPREQLDALLDGINATGYGLTFGVHSRIDETIQHLSERIHAGNLYVNRNVIGAVVGV 1089 Query: 426 APFGGVGLSG 435 PFGG+GLSG Sbjct: 1090 QPFGGMGLSG 1099 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: 1435 Number of extensions: 72 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 471 Length of database: 1335 Length adjustment: 41 Effective length of query: 430 Effective length of database: 1294 Effective search space: 556420 Effective search space used: 556420 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: 55 (25.8 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