Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 216 bits (551), Expect = 1e-60 Identities = 165/481 (34%), Positives = 241/481 (50%), Gaps = 32/481 (6%) Query: 34 FGRHYPLYIGGEWVDTKERMVSLNPSAPS-EVVGTTAKAGKAEAEAALEAAWKAFKTWKD 92 F Y +IGG+WV N S + + ++ + E AL+AA A W Sbjct: 15 FKEKYANFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAAKDAWGK 74 Query: 93 WPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARAALR 151 +RS +LL+ A + + L +E GK E +AD+ +D Y+A Sbjct: 75 TSVTERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRA 134 Query: 152 YRYPAVEVVPYPGEDNESFYVPLGAGVV--IAPWNFPVAIFTGMIMGPVAVGNTVIAKPA 209 A ++ + S++ P GVV I PWNFP+ + I +A GN V+ KPA Sbjct: 135 QEGSAADI----DGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPA 190 Query: 210 EDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIY 269 E V + E+ + PPGV+N + G G E G L R + FTGS EVG I Sbjct: 191 EQTPVSILVLLELIEDL-LPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHIL 249 Query: 270 EAAGRLAPGQTWFKRAYVETGGKD-----AIIVDETADF-DLAAEGVVVSAYGFQGQKCS 323 + A T VE GGK A ++D+ ++ D A EG++++ + QG+ C+ Sbjct: 250 KCAAESLIPST------VELGGKSPNLYFADVMDQEDEYLDKAVEGMLLAFFN-QGEVCT 302 Query: 324 AASRLILTQGAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNE 382 SR+++ + Y+ +E+VL RA+ + G P + +G S EQ K+LSY+ IGK+E Sbjct: 303 CPSRVLIQESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDE 362 Query: 383 G-QLVLGGK--RLEGE---GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALE 436 G Q++LGG +LEGE GY+I+PT+ + K RI QEEIFGPV+SV KD AEAL Sbjct: 363 GAQVLLGGSLCQLEGEQSKGYYISPTIM-KGHNKMRIFQEEIFGPVISVTTFKDEAEALA 421 Query: 437 VANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAK 496 +ANDT YGL GV++R + R G ++ N A FGG+K SG + Sbjct: 422 IANDTEYGLGAGVWTRDMNRAQRMGRGIQAGRVWIN--CYHAYPAHAAFGGYKKSGIGRE 479 Query: 497 T 497 T Sbjct: 480 T 480 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: 599 Number of extensions: 35 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: 506 Length adjustment: 35 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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 Apr 09 2024. 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