Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= BRENDA::Q8BH00 (487 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 294 bits (752), Expect = 5e-84 Identities = 164/485 (33%), Positives = 269/485 (55%), Gaps = 9/485 (1%) Query: 8 LMLENFIGGKFLPC--NSYIDSYDPST-GEVYCKVPNSGKEEIEAAVEAAREAFPAWSSR 64 L +N+I G++L + ++S++P+ E+ P S ++ + AV AAR+A+ +W Sbjct: 5 LNCQNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKV 64 Query: 65 SPQERSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHH 124 R+ + R+ ++L Q EELAQ S++ GK +T AR D+ V + A Sbjct: 65 PAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGRRL 123 Query: 125 VSECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTS 184 + T TVR P+G+ LI+PWN P+ + WK PA+ GNTVI KP+E T Sbjct: 124 FGQTTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTP 183 Query: 185 VTAWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSA 244 A ++ AG+PPGVIN+V G G G+ALV HP + L+SFTGS T + + Sbjct: 184 ACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCG 243 Query: 245 PHCKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFL 304 K++ LE+GGKN ++ EDA+LE + + +F G+ C TSR+ + R I +F Sbjct: 244 RTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFT 303 Query: 305 KRFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLP 364 E T + ++G ++P ++G +I+ L++V Y+ A+ EGA+IL G ++ Sbjct: 304 TMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIG---GEIVTE 360 Query: 365 LRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVW 424 + + GYF PT++ ++ + R EEIFGPV ++ + EE I N +YGL+++V+ Sbjct: 361 GQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVY 420 Query: 425 SKDVGRIHRVAKKLQSGLVWTNCWLI-RELNLPFGGMKSSGIG-REGAKDSYDFFTEIKT 482 ++D+ R + ++ G+ + N I E++LPFGG+K +G G RE + D FTE K+ Sbjct: 421 TRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKS 480 Query: 483 ITIKY 487 + + + Sbjct: 481 VYVDF 485 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: 532 Number of extensions: 27 Number of successful extensions: 4 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: 498 Length adjustment: 34 Effective length of query: 453 Effective length of database: 464 Effective search space: 210192 Effective search space used: 210192 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 Apr 09 2024. 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