Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 3608023 Dshi_1430 aldehyde dehydrogenase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >FitnessBrowser__Dino:3608023 Length = 487 Score = 296 bits (759), Expect = 8e-85 Identities = 181/460 (39%), Positives = 248/460 (53%), Gaps = 12/460 (2%) Query: 38 DCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQH 97 D +P G + +I +C + RAV AR F G WSRL R + + + H Sbjct: 29 DVTNPATGEKIAQIPACGPDEVDRAVTAARRAFEDGEWSRLTAVDRGRLLHKLGEAITAH 88 Query: 98 AEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREP 157 +ELA E D GKP++ + D+ AA+ + G A DK++ E EP Sbjct: 89 GQELAEWEAKDTGKPLAQA-RADMVAAARYFEYYGAAADKVHGETIPFLSGYQVQTIFEP 147 Query: 158 VGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVL 217 GV G I+PWN+P M PAL+ GN+VVLKP+E + LT LRIA LA+E G P G + Sbjct: 148 YGVTGHIIPWNYPAQMFGRSCAPALAMGNAVVLKPAEDACLTPLRIAELALEVGFPGGAI 207 Query: 218 NVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVF 277 NV+ GYG G AL H DVD L FTGS ++ + + +++ LE GGKSP IVF Sbjct: 208 NVVTGYGQEAGAALTTHRDVDFLSFTGSPEVGVMIQTAAARNHI-GCTLELGGKSPQIVF 266 Query: 278 ADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV---IEALKGWKPGNP 334 ADA DL AA + I N G+ C+AGSR L++R I D L + EAL P Sbjct: 267 ADA-DLDAAIPVLLNGIVQNGGQTCSAGSRALIQRDIFDAVLARLKAGFEAL----TAAP 321 Query: 335 LDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEET-GGTYVEPTIFDGVSN 393 N+G L+ +Q V +I G A LVA G+ + G++V P +F V Sbjct: 322 WQENGNLGPLISHKQKRRVEGFIAEGGGADAPLVARGRIAASASEAGSFVAPALFGPVIE 381 Query: 394 AMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAHLTAKALRAGSV 453 +A+EE+FGPVLS I F AI IAN T YGL A+VW+ D + AK LR G V Sbjct: 382 GHVLAREEVFGPVLSCIPFTDEADAIRIANATDYGLVASVWSADGGRQMRLAKRLRVGQV 441 Query: 454 WVNQYD-GGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKS 492 ++N Y GG + PFGG ++SG+GR+K A +++++K+ Sbjct: 442 FLNCYGAGGGIELPFGGMRKSGHGREKGFAALHEFSQIKT 481 Lambda K H 0.316 0.132 0.389 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: 628 Number of extensions: 41 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: 497 Length of database: 487 Length adjustment: 34 Effective length of query: 463 Effective length of database: 453 Effective search space: 209739 Effective search space used: 209739 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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