Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011189156.1 DP_RS09800 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000025945.1:WP_011189156.1 Length = 504 Score = 199 bits (506), Expect = 2e-55 Identities = 157/494 (31%), Positives = 228/494 (46%), Gaps = 48/494 (9%) Query: 46 WVDTKERMVSL-------NPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98 WVD + R NPS EV A E E A+ +A A+ W P R Sbjct: 8 WVDNQWRRSKTTSYADLYNPST-GEVTAQVAHCTAEEVEEAIASAAAAYPGWAATPVGKR 66 Query: 99 SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158 ++ + L+ + EL L E GKN E+ DV + + IE+ A + P++ Sbjct: 67 VQIFFRMKMLVDQHLEELTDILCREQGKNRAESMGDVLKVNEVIEFACGAPHLMKGPSLF 126 Query: 159 VVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAV--GNTVIAKPAEDAVVVG 216 V G D PLG I PWNFP I G M P+ + GNT++ K A Sbjct: 127 NVSN-GYDTVQQMRPLGVFAGIVPWNFPAMIPHGW-MAPICMVTGNTMVLKAASYVPRTA 184 Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276 ++ E++ EAG PPGV+N + E L+ HP + ++F GS VG IYE A A Sbjct: 185 MRLMELWQEAGLPPGVLNLVTANRTEA-EILLRHPEIKGVSFVGSTTVGRHIYETA--TA 241 Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336 G KR K+ +V E + + A+G++ + G G +C A +++ + + Sbjct: 242 NG----KRVQALCAAKNHALVLEDCNLERTAQGIINAFCGCAGARCMALPVIVVQESIAD 297 Query: 337 PVLERVLKRAERLSVGPAE-ENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLE- 393 ++ER+ A++L++G A +GP+V+A ++ +L +I G EG LVL G+R Sbjct: 298 KLVERITYHAKKLTMGKAWLPETGMGPIVNAGHKKSILDWIARGITEGADLVLDGRRPVV 357 Query: 394 ----GEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449 GYFI PT+F V P+ I EEIFGPVLSV RVKDFAE + + N PY + Sbjct: 358 AAGCENGYFIGPTIFDNVTPEMSIGSEEIFGPVLSVKRVKDFAEGIALMNANPYANGSVI 417 Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQ-----PFGGFKLSGT------NAKTG 498 Y+ FH N F + G +VG+ P G F +G + T Sbjct: 418 YTES---------GFHARN--FVAQTDGGMVGINVGIPVPVGIFGFTGQKKSFYGDLHTM 466 Query: 499 ALDYLRLFLEMKAV 512 D R + E K V Sbjct: 467 GQDGFRFYTEQKTV 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: 551 Number of extensions: 29 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: 504 Length adjustment: 34 Effective length of query: 482 Effective length of database: 470 Effective search space: 226540 Effective search space used: 226540 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 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