Align Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= curated2:A8GHZ8 (474 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 150 bits (380), Expect = 2e-40 Identities = 142/461 (30%), Positives = 215/461 (46%), Gaps = 32/461 (6%) Query: 13 TGQGALLPVYNPATG-EVVVQVAEASAEQVDQAVLAADAAFEHWGQTTPKERAEHLLKLA 71 T GA + V NPA +VV A + V++A+ A AA W + RA L A Sbjct: 590 TSAGATVQVTNPADRRQVVGSYVSADSATVEKALANAVAAQHGWDRLPAASRAAILEHAA 649 Query: 72 DLIDSHAETFARLESINCGKPYHCVLNDELPGVADVFRFFAGASRCLSGLAAGEYLAGHT 131 + +++ F L GK + E+ AD R++A +R G E L G T Sbjct: 650 EQLEARRGEFIALCVREAGKGLPDAIA-EIREAADFLRYYATMARRYFGQP--EQLPGPT 706 Query: 132 ---SMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEQTPLTTFKLAELA 188 + + + GV I+PWN+PL + ++A ALAAGN V+ KP+EQT L +L Sbjct: 707 GESNQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLL 766 Query: 189 --AGLFPPGVLNVLFGRGASVGDRLTGHNKVRMVSLTGSIATGEHI---IGHTASGIKRT 243 AG+ P VL L G GA+VG LT +V V+ TGS T I + + I Sbjct: 767 HEAGV-PADVLQYLPGDGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAAL 825 Query: 244 HMELGGKAPVLVFDDADLQQVVEGIRSFGFYNAGQDCTAACRIYAQKGIYPQLVKALGEA 303 E GG+ ++ A +Q+V+ S F +AGQ C+AA +Y Q+ I ++ L A Sbjct: 826 IAETGGQNAMIADSSALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAMLAGA 885 Query: 304 IGSLKIGPPIDASSELGPLITAQHLERVVGFVER----AKALPHVQV---VTGGERVNGP 356 + LK+G P S+++GP+I + +V R AK + V + TG P Sbjct: 886 MAELKVGDPAQLSTDVGPVIDEDARKILVDHAARMDQEAKKIGEVALDPATTGNGTFFAP 945 Query: 357 GYYFQPTLLAGARQEDEIVQREVFGPVVTVTPF--DDEAQVLAWANESDYGLASSLWTRD 414 Y P L + RE+FGPV+ V + + +V+ N + YGL + +R Sbjct: 946 RAYEIPGLAT--------LTREIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSRI 997 Query: 415 VGRAHRLSARLQYGCTWVNTHFM--LVSEMPHGGQKLSGYG 453 + +R + G +VN + + +V P GG+ LSG G Sbjct: 998 DDTVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSGTG 1038 Lambda K H 0.320 0.136 0.410 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: 1028 Number of extensions: 48 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 474 Length of database: 1074 Length adjustment: 39 Effective length of query: 435 Effective length of database: 1035 Effective search space: 450225 Effective search space used: 450225 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 (21.8 bits) S2: 55 (25.8 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