Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF519 PS417_02645 aldehyde dehydrogenase
Query= curated2:Q2G9T9 (471 letters) >FitnessBrowser__WCS417:GFF519 Length = 496 Score = 200 bits (509), Expect = 8e-56 Identities = 140/450 (31%), Positives = 227/450 (50%), Gaps = 26/450 (5%) Query: 9 HEPATGAEV----WRGKVGDVEEVVARARRAWPAWAAQPLATRIELVRRFANEVRKDADN 64 H P G+ + W G +VE+ V+RA A+ AW P R ELVR+F + +R+ + Sbjct: 24 HSPIDGSRIGSVHWEG-AAEVEQQVSRAEHAFEAWRKVPAPRRGELVRQFGDVLREYKAD 82 Query: 65 LATMISRETGKPLWEARTEVDSVVN----KVEISIRAYADRTSQRKLDSALQGTAALRHK 120 L ++S E GK E EV +++ V +S + Y + + ++ T Sbjct: 83 LGELVSWEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRET----WH 138 Query: 121 PHGVLAVLGPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRA-----G 175 P GV+ V+ +NFP + + AL+ GNAV++KPSEKTP T F R G Sbjct: 139 PLGVVGVISAFNFPVAVWAWNTTLALVCGNAVIWKPSEKTPLTALACQALFERVLKKFDG 198 Query: 176 IPAAVVQVLIGGPEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASNPGKIVALEMGGNN 235 P + QV+IGG + G ALV + + TGS G + K+A+ + + LE+GGNN Sbjct: 199 APEYLSQVIIGGRDAGAALVDDPRVALISATGSTRMGREVAPKVAARFARSI-LELGGNN 257 Query: 236 PIVVWDTPKIEDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGA 295 +++ + ++ A I+ SA +AGQRCT RRLI S+ E++ +K ++ +G Sbjct: 258 AMILGPSADLDMAVRAILFSAVGTAGQRCTTLRRLIAHESVKAEIVTRLKAAYSKVRIGH 317 Query: 296 PFDDPAPFMGPVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRP---FLSPAIIDVT 352 P + +GP+ID D + ++ LS GG+ +L++ P ++SPAI+++ Sbjct: 318 PLE--GNLIGPLIDKHGFDNMQDALEQALSEGGKVFGGKRQLEDQFPNAYYVSPAIVEMP 375 Query: 353 AVADRPDVELFGPLLQVVRVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRA-- 410 +D E F P+L V+ DF+EA+ N GLS+ + D ++ +F + + + Sbjct: 376 EQSDVVCTETFAPILYVIGYSDFNEALRLNNAVPQGLSSCIFTTDVREAEQFMSAVGSDC 435 Query: 411 GVVNWNRPTNGASSAAPFGGVGLSGNHRPS 440 G+ N N +GA FGG +G R S Sbjct: 436 GIANVNIGPSGAEIGGAFGGEKETGGGRES 465 Lambda K H 0.319 0.135 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: 601 Number of extensions: 35 Number of successful extensions: 8 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: 471 Length of database: 496 Length adjustment: 34 Effective length of query: 437 Effective length of database: 462 Effective search space: 201894 Effective search space used: 201894 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