Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 177 bits (450), Expect = 6e-49 Identities = 147/464 (31%), Positives = 230/464 (49%), Gaps = 27/464 (5%) Query: 3 HWIAGEWVQG-QGEEFVSLSPYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAER 61 ++I G++V +G F ++SP + +V + +T E ++ AV AA AF W K ER Sbjct: 16 NYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTER 75 Query: 62 EAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEAAAMAGK----IAISIRAYHDRTG 117 I+ A+++++N E +A V + GK + ET + A IRA Sbjct: 76 SIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSLS 135 Query: 118 EATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTG 177 E + ++ H P+GV+A P+NFP + + PAL AGN VV KP+E TP + Sbjct: 136 ELDQNTVS---LIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSI 192 Query: 178 ELAMKLWEEAGLPKGVINLVQG-AKETGIALADAKGIDGILFTGSANTGHILHRQFAGQP 236 + M+L + LP GV+N+V G E G AL + FTGS TG ++ Q+A + Sbjct: 193 MVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLV-MQYATEN 250 Query: 237 GKMLALEMGGNNP-----MVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEK 291 + LE+GG +P V++++ LD V + A ++ G+ CTC RL + + Sbjct: 251 IIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFA-LNQGEICTCPSRLLIQ-EDI 308 Query: 292 GDALITKLVEATKNIRMDQPFAEPAPFMGPQISVA-----AAKFILDAQANLQSLGGESL 346 + I K++E TK I++ P + MG Q S AA L + + L G + Sbjct: 309 YEKFIAKVIERTKAIKIGSPL-DRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEI 367 Query: 347 IE--AKAGEAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSA 404 E + G ++ P I N + EE FGP+L V ++ +++A+E+ANDT +GL A Sbjct: 368 NELPGELGGGYYIKPTIFKGHNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGA 427 Query: 405 GLVSTDDQEWEYFVDHIRAGIVNRNRQLTGASGDAPFGGPGASG 448 G+ + D E I+AG V N+ +G APFGG SG Sbjct: 428 GVWTRDAHELYQVPRAIQAGRVWVNQYHAYPAG-APFGGYKQSG 470 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: 551 Number of extensions: 33 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: 485 Length of database: 501 Length adjustment: 34 Effective length of query: 451 Effective length of database: 467 Effective search space: 210617 Effective search space used: 210617 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 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