Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= BRENDA::Q72IB9 (516 letters) >MicrobesOnline__882:208821 Length = 464 Score = 152 bits (383), Expect = 3e-41 Identities = 129/435 (29%), Positives = 190/435 (43%), Gaps = 19/435 (4%) Query: 65 VGTTAKAGKAEAEAALEAAWKAF-KTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYE 123 VG +AEA AALE A P +R +L + A LMR L V E Sbjct: 15 VGEVPLMSEAEAFAALERAHALHGDPAHRIPAHERLAILERLATLMRTHAEALVRDAVRE 74 Query: 124 VGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYV---PLGAGVVI 180 GK W ++ +V AID + + AR + V + P + P G + I Sbjct: 75 GGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLAFTVREPRGVVLAI 134 Query: 181 APWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVG 240 + +N PV + + A G V+ KPA + V + HEAG P LP Sbjct: 135 SAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEAGVPEAWATMLP-CA 193 Query: 241 EEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDET 300 LV PR F++F GS VG + +LAPG T +E GG +++D + Sbjct: 194 AATAEKLVADPRVAFLSFIGSSRVG---WHLRSKLAPGAT----CALEHGGAAPVVLDAS 246 Query: 301 ADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG-PAEENPD 359 AD D A ++ + GQ C + R+ ER+ A +L G P + Sbjct: 247 ADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPTGDPMRHDTA 306 Query: 360 LGPVVSAEQERKVLSYIEIGKNEGQLVL-GGKRLEGEGYFIAPTVFTEVPPKARIAQEEI 418 +GP++ + +V ++E + G VL GG L Y +PTV + P R+A+ E+ Sbjct: 307 VGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSETLY--SPTVVYDPPQGCRLARNEV 364 Query: 419 FGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE-HLEWARREFHVGNLYFNRKITG 477 FGPV++V +D EA+ AND P+ V++R + L+ ARR G + + T Sbjct: 365 FGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVMVNDH--TA 422 Query: 478 ALVGVQPFGGFKLSG 492 V PFGG SG Sbjct: 423 FRVDWMPFGGRGESG 437 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: 517 Number of extensions: 24 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: 464 Length adjustment: 34 Effective length of query: 482 Effective length of database: 430 Effective search space: 207260 Effective search space used: 207260 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