Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= curated2:Q87L22 (485 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 175 bits (444), Expect = 3e-48 Identities = 146/466 (31%), Positives = 223/466 (47%), Gaps = 31/466 (6%) Query: 3 HWIAGEWVQG-QGEEFVSLSPYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAER 61 ++I G+WV +G+ F ++SP + VI ++AE V+ A+ AA AA W + AER Sbjct: 21 NFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAER 80 Query: 62 EAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEAAAMA----GKIAISIRAYHDRTG 117 +L A+++++ + +A V + GKPI ET+ +A A +RA Sbjct: 81 SLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGIS 140 Query: 118 EATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTG 177 E + H PLGV+A P+NFP + + PAL AGN V+ KP+EQTP + Sbjct: 141 EIDHDTVAYHF---HEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMS- 196 Query: 178 ELAMKLWEEAG--LPKGVINLVQG-AKETGIALADAKGIDGILFTGSANTGHILHRQFAG 234 M L + G LP GV+N++ G E G LA K I + FTG TG ++ Q+A Sbjct: 197 --VMVLVDMIGDLLPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLI-MQYAS 253 Query: 235 QPGKMLALEMGGNNPMVISDNYGDLDATVYTIIQSAF----ISAGQRCTCARRLYVPFGE 290 + + LE+GG +P + + D D + F ++ G+ CTC R V E Sbjct: 254 ENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQ--E 311 Query: 291 K-GDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFIL-------DAQANLQSLG 342 K D + + V K I+ P +PA +G Q S + IL A + + G Sbjct: 312 KIYDRFMERAVARVKKIKQGNPL-DPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGG 370 Query: 343 GESLIEAKAGEAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGL 402 G + + + +V P I++ N + EE FGP+L V ++ ++A+E+ANDT +GL Sbjct: 371 GRADVGPELAGGFYVQPTILEGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGL 430 Query: 403 SAGLVSTDDQEWEYFVDHIRAGIVNRNRQLTGASGDAPFGGPGASG 448 AG+ + + F I AG V N A FGG SG Sbjct: 431 GAGVWTRNGTRAYRFGRAIEAGRVWTNCYHL-YPAHAAFGGYKQSG 475 Lambda K H 0.316 0.134 0.397 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: 533 Number of extensions: 27 Number of successful extensions: 5 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: 485 Length of database: 506 Length adjustment: 34 Effective length of query: 451 Effective length of database: 472 Effective search space: 212872 Effective search space used: 212872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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