Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 242 bits (617), Expect = 3e-68 Identities = 159/460 (34%), Positives = 236/460 (51%), Gaps = 16/460 (3%) Query: 41 VIDGERYETENKIVSINPANKE-EVVGTVSKATQDHAEKAIQAAAKAFET--WRYTDPEE 97 VIDG+ E + N + ++ +V+ V+ D E+A+ A AFE WR P + Sbjct: 24 VIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQ 83 Query: 98 RAAVLFRAVAKVRRKKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQMIELAKGK 156 + AVLFR + R E + L + GKP ++A + D AI+ +YA + ++ G+ Sbjct: 84 KKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYA-EALDKVYGE 142 Query: 157 PVNSREGERNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAA 216 S + V+ P GV I PWNF + + GN+VVLKPA +P+ A Sbjct: 143 VGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202 Query: 217 KFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQP 276 K + E+GLP GV+N +PG G G+ L +I FTGS VG R+ E +A+ Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSAR--- 259 Query: 277 GQTHLKQVIAEMGGKDTVVVDEDC-DIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYD 335 ++LK+V E+GGK +V DC D+E AAQ+ F G+ C+A SR +V + D Sbjct: 260 --SNLKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKD 317 Query: 336 EVLKRVIEITESKKVGEPDSADVYMGPVIDQASFNKIMDYIEIGKEEG-RLVSGGK--GD 392 L RVIE+ + KVG+P G ++ + N +DYI +G R V GG+ Sbjct: 318 AFLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQ 377 Query: 393 DSKGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITK 452 ++ G+++EPTIF + P L +EE+FGPV+ SS DEA+ +AN+T YGL + T Sbjct: 378 EAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTA 437 Query: 453 NRDHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 492 + R + G ++ N I PFGGFK SG Sbjct: 438 DVSKALRGARRLKAGLVWVNGWDACDIT--MPFGGFKQSG 475 Lambda K H 0.315 0.133 0.382 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: 563 Number of extensions: 24 Number of successful extensions: 6 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: 499 Length adjustment: 34 Effective length of query: 482 Effective length of database: 465 Effective search space: 224130 Effective search space used: 224130 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