Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate SMc04397 SMc04397 L-sorbosone dehydrogenase, NADP dependent protein
Query= BRENDA::Q8BH00 (487 letters) >FitnessBrowser__Smeli:SMc04397 Length = 504 Score = 321 bits (822), Expect = 4e-92 Identities = 175/463 (37%), Positives = 263/463 (56%), Gaps = 9/463 (1%) Query: 25 IDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPA--WSSRSPQERSLVLNRLADVLEQ 82 I+ P G V + + K + E A+ AAR AF W + ERSL+L R AD++ Sbjct: 37 IERVAPGHGVVVSRYQAAAKADAERAIAAARRAFDEGPWPRMTASERSLILLRAADMIAA 96 Query: 83 SLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQMSHLGCMHYTVR 142 +ELA ++ + GK ++ A+ ++ + +R+ A+ E G + +R Sbjct: 97 RADELAFLDAVESGKPISQAKG-ELAGAADIWRYAAALARELSGESYNTLGEGTLGVVLR 155 Query: 143 TPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPG 202 P+G+ +I+PWN P +++ K+ A+AAG T + KPSE+TS + + ++L+ AGVP G Sbjct: 156 EPIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTSASTLVLGEILEAAGVPQG 215 Query: 203 VINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAII 262 V+NI+ GTGP G L +HP V ++SFTGS + +A KK+SLELGGKNP I+ Sbjct: 216 VVNIIVGTGPEAGAPLTTHPHVDMVSFTGSTGIGQLTMANAAQTLKKVSLELGGKNPQIV 275 Query: 263 FEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDP 322 F DANL+E I A V ++ N GE C SR+ + R I E R + K KVG P DP Sbjct: 276 FPDANLDEFIDAAVFGAYFNAGECCNAGSRLILHRDIAEEVTARIASLSAKVKVGDPLDP 335 Query: 323 SANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPTVITDIK 382 +GA+I+ HL+K+ YV A EGARI G L + G FM PT+++ ++ Sbjct: 336 ETQVGAIITPQHLQKIAGYVSSASNEGARIAHGGTTLDLGM------GQFMAPTILSAVR 389 Query: 383 DESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGL 442 E EE+FGPV V+ F+ EE I ANS+ YGL+A VWS+D + +++++G Sbjct: 390 PEMAVAREEVFGPVLSVLTFEKTEEAIRIANSIDYGLSAGVWSRDFDTCLTIGRRVRAGT 449 Query: 443 VWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITI 485 VW N ++ LPFGG + SG+GRE + + + +TE KT+ + Sbjct: 450 VWMNTFMDGASELPFGGYRQSGLGRELGRHAVEDYTETKTLNM 492 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: 534 Number of extensions: 21 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: 504 Length adjustment: 34 Effective length of query: 453 Effective length of database: 470 Effective search space: 212910 Effective search space used: 212910 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 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