Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 244 bits (622), Expect = 7e-69 Identities = 162/483 (33%), Positives = 245/483 (50%), Gaps = 29/483 (6%) Query: 42 IGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRL 101 I G V++ + +LNP A +EV+ A G+AE A+ AA +AF W P R++L Sbjct: 6 INGRQVESASTIANLNP-ANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRAKL 64 Query: 102 LLKAAALMRRRKRELEATLVYEVGKN-WVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160 L K L+ + E+ + G++ W V A D ++A V+ Sbjct: 65 LRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCH-----VDGE 119 Query: 161 PYPGED--NESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAK 218 YP D N + Y P+G +I+PWN P T +A GNT + K +E + + + Sbjct: 120 TYPTNDHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADR 179 Query: 219 VFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPG 278 + ++ EAG P GV N + G G VG LV+HP R ++FTGS G +I ++ G Sbjct: 180 LGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGG----- 234 Query: 279 QTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPV 338 K+ +E GGK I+ + DF+ A + +V+ YG G+ C+ +R+++ G Y+ Sbjct: 235 ---LKKYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRF 291 Query: 339 LERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGY 397 + + +R ++ VG P +E ++GP+++ + +KV SYIE+G +EG V+ G EG Sbjct: 292 VAALAERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGL 351 Query: 398 --------FIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449 F+ PTV +V R+AQEEIFGPV VIR KD AEAL++AN T YGL V Sbjct: 352 APHLKNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYV 411 Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEM 509 ++ G ++ N + L QPFGG K SGT + G Y FLE+ Sbjct: 412 WTENGARAIRMAEGIEAGLVFVNSQNVRDL--RQPFGGIKGSGTGREGGHYSY-EAFLEV 468 Query: 510 KAV 512 K V Sbjct: 469 KNV 471 Lambda K H 0.319 0.137 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: 546 Number of extensions: 32 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: 516 Length of database: 485 Length adjustment: 34 Effective length of query: 482 Effective length of database: 451 Effective search space: 217382 Effective search space used: 217382 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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