Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_104914315.1 C3B54_RS06570 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_002950575.1:WP_104914315.1 Length = 497 Score = 235 bits (599), Expect = 3e-66 Identities = 148/482 (30%), Positives = 242/482 (50%), Gaps = 19/482 (3%) Query: 40 LVIDGERYETENKIVSINPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERA 99 L IDGE T +I INP++K E+ V+ + HA +A+ AA ++ + WR+ P RA Sbjct: 21 LFIDGEWLRTGQEIPVINPSDKSEIT-KVADGSGGHALEALAAADRSAQQWRHWAPRARA 79 Query: 100 AVLFRAVAKVRRKKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVN 159 + A + + F+ ++ E+GKP EA + + F +YA Q+ L Sbjct: 80 DLFHLAHGLLIERADAFADVMTMESGKPRAEALGEFNLSAGFFLWYAEQVAHLHGRYQEG 139 Query: 160 SREGERNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFV 219 S G R + P G + ++ PWNF + A A + G TVV+K A P+ AA F+ Sbjct: 140 SPGGYRVIETHQPVGPSFLVTPWNFPMLMSARKAGAALAAGCTVVIKSARETPLTAALFI 199 Query: 220 EVLEESGLPKGVVNFV-PGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQ 278 + L+E+G P GVVN + + AEV + ++ + ++FTGS VGT + ++A+ + Sbjct: 200 DTLQEAGFPAGVVNLIHTSNSAEVSEQIMADSRLKKVSFTGSSAVGTVLLKQASNL---- 255 Query: 279 THLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVL 338 + E+GG +V +D D++LA + F AGQ C A +R ++HE + +E Sbjct: 256 --IINSSMELGGDGPFIVLDDADVDLAVREAVICKFRNAGQACVAANRIILHESIAEEFT 313 Query: 339 KRVIEITESKKVGEPDSADVYMGPVIDQASFNKIMDYIE-IGKEEGRLVSGGKGDDSKGY 397 ++ + T + KVG+ +V +GP+I + N++ +E G L++GG D +G+ Sbjct: 314 EKFLAATAALKVGDGFDPEVSVGPIITERQLNRVSGLVESFQSAGGTLLAGGNVIDGEGF 373 Query: 398 FIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHI 457 F EPT+F +E+F P+ A V++ DEAL AN+T YGL+ V +K+ + Sbjct: 374 FFEPTVFRFDSYDHDFCNDELFAPIAALYTVTTVDEALRFANDTHYGLSAYVFSKDLSRV 433 Query: 458 NRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG--------GPDYLALHMQA 509 + G + NR PFGG K SG +AG P Y+AL + Sbjct: 434 VTVAERLDFGMVGVNRGIMSDPKA--PFGGIKESGLGREAGHEGIYEFLEPKYIALTIDE 491 Query: 510 KT 511 ++ Sbjct: 492 RS 493 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: 597 Number of extensions: 21 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 516 Length of database: 497 Length adjustment: 34 Effective length of query: 482 Effective length of database: 463 Effective search space: 223166 Effective search space used: 223166 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 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