Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 355 bits (910), Expect = e-102 Identities = 182/455 (40%), Positives = 272/455 (59%), Gaps = 5/455 (1%) Query: 29 DPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSLVLNRLADVLEQSLEELA 88 DP+TGE +G ++++AAV AAREAFP W+ +P +RS L+R A+VL E+ A Sbjct: 42 DPATGEEVHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDFA 101 Query: 89 QAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQMSHLGCMHYTVRTPVGIA 148 +AES GK L L R D+P ++ N FFA + H + Y R P+G+ Sbjct: 102 RAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRREPIGVV 161 Query: 149 GLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPGVINIVF 208 G I+PWN PL + WK+ PAIAAGNT++ KP+E+T +T+ +F + +AG+P GVINIV Sbjct: 162 GSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINIVT 221 Query: 209 GTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFEDANL 268 GTG GE LV HP+V ++SFTGS +R+ +++ K+L LELGGK P ++F+DA+L Sbjct: 222 GTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLELGGKAPFVVFDDADL 281 Query: 269 EECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDPSANMGA 328 E + V + N G+ C +R +VQR +Y EF+ R ++G P P ++G Sbjct: 282 EAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLGDPFAPGTDLGP 341 Query: 329 LISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPTVITDIKDESRCM 388 LIS H ++V +V +A+ AR++ G Q L + G + PT+I +S + Sbjct: 342 LISHVHRDRVAGFVDRARAY-ARVVTGGEAPQGEL----KNGAYYRPTLIAGAAQDSEIV 396 Query: 389 TEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGLVWTNCW 448 EIFGPV V+PFDS++E I AN YGLAA+ WS+DV R +R +++++G VW N Sbjct: 397 QSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGCVWVNDH 456 Query: 449 LIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTI 483 + +P GG K SG G++ + S++ +T+IK + Sbjct: 457 IPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHV 491 Lambda K H 0.319 0.134 0.404 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: 535 Number of extensions: 24 Number of successful extensions: 3 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: 487 Length of database: 511 Length adjustment: 34 Effective length of query: 453 Effective length of database: 477 Effective search space: 216081 Effective search space used: 216081 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: 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