Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_018125680.1 B149_RS0113400 betaine-aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000375485.1:WP_018125680.1 Length = 491 Score = 249 bits (636), Expect = 2e-70 Identities = 171/487 (35%), Positives = 257/487 (52%), Gaps = 29/487 (5%) Query: 40 LYIGGEWVDT---KERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKT--WKDWP 94 +YI GEWV KER + LNP S V+ + +AG+ E A+ AA +AF W P Sbjct: 6 MYIDGEWVAADSGKEREI-LNPF-DSSVIASVPEAGRGETRRAIAAARRAFDEGGWPQTP 63 Query: 95 QEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRY 154 +R+RL+ K A L+ R EL + GK E+ D+ + Y+A A + Sbjct: 64 AAERARLVFKLAELIERDHEELARLESLDTGKTVEESRWDMDDIAGIFRYFAGLADK--- 120 Query: 155 PAVEVVPYPGEDNESFYV--PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDA 212 EV+ P D S+ + P+G I+PWN+P+ + + +A G TV+ KP+E Sbjct: 121 DGGEVIESPVPDTTSYVMREPVGVCGQISPWNYPLLQASWKMAPALAAGCTVVMKPSEIT 180 Query: 213 VVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAA 272 + KV E+ EAGFP GVVN + G G EVGA L E I+FTG +E G I AA Sbjct: 181 PLTTIKVTELAEEAGFPKGVVNTVLGPGAEVGAELSESHDVDLISFTGGIETGKTIMRAA 240 Query: 273 -GRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILT 331 G + K+ +E GGK+ I+ + ADFDLA + + + GQ CSA +R+++ Sbjct: 241 TGNV-------KKVALELGGKNPNIIFDDADFDLAVDYALNGVFFHAGQICSAGARILVQ 293 Query: 332 QGAYEPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGG 389 +G ++ +E + KR ER+ +G +++ +GP+ SAE KV +Y EIGK EG +L+LGG Sbjct: 294 EGIHDRFVEELRKRMERIKLGNGFDDDTQMGPLTSAEHLAKVEAYGEIGKKEGAKLLLGG 353 Query: 390 KRLEGE----GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGL 445 R + E GYF PT+F++ RI QEE FGP++++ + EA+ AN T YGL Sbjct: 354 CRPDDEALKDGYFYMPTLFSDCENDMRIVQEETFGPIITIEKFSTEEEAVTRANSTVYGL 413 Query: 446 TGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRL 505 + G ++ +E + G ++ N P+GG+K SG + G + L Sbjct: 414 SAGFWTNDPNRIERVSKALRFGTVWIND--FNVYFVQAPWGGYKQSGLGRELGRMG-LEE 470 Query: 506 FLEMKAV 512 + E+K V Sbjct: 471 YTEVKHV 477 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: 603 Number of extensions: 29 Number of successful extensions: 5 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: 491 Length adjustment: 34 Effective length of query: 482 Effective length of database: 457 Effective search space: 220274 Effective search space used: 220274 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