Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_086509055.1 BZY95_RS05955 aldehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_12580 (497 letters) >NCBI__GCF_002151265.1:WP_086509055.1 Length = 516 Score = 300 bits (768), Expect = 8e-86 Identities = 182/467 (38%), Positives = 250/467 (53%), Gaps = 8/467 (1%) Query: 33 SGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFNSGVWSRLAPSKRKTTMIRFAG 92 +GET + P G L A +RAV +A + W L S+R M Sbjct: 39 AGETITLIDPATGEALLDYRDAGPALVERAVSSASRAQQA--WMALTASERGRRMNAAVR 96 Query: 93 LLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLGL 152 L+ H E LA LE++ GKPI D +V + + DK + EV P L Sbjct: 97 GLEGHEEALAQLESVVAGKPIRDCRG-EVGKVREMFDYYAGWCDKQHGEVIPVPTSHLNY 155 Query: 153 VTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTAIRIAALAIEAGI 212 V P GVVG I PWN P+ W+L PA++ GN VLKPSE +P T++ IA L G+ Sbjct: 156 VRHVPYGVVGQITPWNAPMFTCAWQLAPAIAAGNGAVLKPSELTPFTSVVIARLLERGGL 215 Query: 213 PKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAGGKS 272 PKG++N++ G G + G AL + LVF GS + + L+ +G + LE GGKS Sbjct: 216 PKGLVNIVNGLGPSTGAALTGSEGISKLVFVGSPQSGR-LIAEAGARRLVPSVLELGGKS 274 Query: 273 PNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLVIEALKGWKPG 332 NIVFADA L AA A +AI G+ C AGSRLLV+R + + A G + G Sbjct: 275 ANIVFADA-SLDAAVAGAQAAIFAAAGQSCVAGSRLLVQREVFAEVTERLARAAAGIEVG 333 Query: 333 NPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKR---ILEETGGTYVEPTIFD 389 P D AT +G L + +Q V IE + GA+++ GG R + EE G ++ PT+ Sbjct: 334 LPGDEATRMGPLQNARQYAHVTRMIEDAVAAGARVIVGGSRPAGLPEEARGYFLAPTVLV 393 Query: 390 GVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAHLTAKALR 449 V+ M+IA+EE+FGPVL + FD A+ +AN T +GLA AVWT+D ++AH A LR Sbjct: 394 DVTPEMEIAREEVFGPVLVAMPFDDEADAVRLANATRFGLAGAVWTQDPARAHRVAAQLR 453 Query: 450 AGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTWIK 496 AG+VW+N Y + +PFGGF SG GR L +YT +S W++ Sbjct: 454 AGTVWINGYKAISVMSPFGGFGDSGFGRSSGLDGLREYTLPQSVWVE 500 Lambda K H 0.316 0.132 0.390 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: 679 Number of extensions: 36 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: 497 Length of database: 516 Length adjustment: 34 Effective length of query: 463 Effective length of database: 482 Effective search space: 223166 Effective search space used: 223166 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 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