Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_057507192.1 ABB28_RS02945 aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001431535.1:WP_057507192.1 Length = 460 Score = 206 bits (523), Expect = 2e-57 Identities = 138/445 (31%), Positives = 220/445 (49%), Gaps = 21/445 (4%) Query: 56 AADVDKAVKAARKAF-DQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKP-- 112 AA +++ + AA + F D+ W + P R ++ +LA LM+ + LA + GKP Sbjct: 21 AAALEQKLSAAERVFKDRDGW--LPPHERIAILRRLAALMDAKRDHLALQIAREGGKPLP 78 Query: 113 --INETTNGDIPLAIEHMRYYAGWCTKITGQTIPV-----SGAYFNYTRHEPVGVVGQII 165 I ETT AI+ + A G+ IP+ + + +T EP+G+V I Sbjct: 79 DAIIETTR-----AIDGVHNAADELRNFGGREIPMGLSAAAVGRWAFTTREPIGIVAAIS 133 Query: 166 PWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGE 225 +N PL + + ++ A+A GC +++KPA TPLS L L ++ +AG P G Sbjct: 134 AFNHPLNLIVHQVAPAIAVGCPVIIKPASATPLSCLDLVAMVHEAGLPEPWCQSFMPEGN 193 Query: 226 DAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAI 285 D EAL + V ++F GS +G + S A R LE GG +P I+ +A+L + I Sbjct: 194 DLAEALATDKRVAFLSFIGSARVGWSLHSKLAHGA-RSALEHGGVAPAIVDRNADLSRII 252 Query: 286 PGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSK 345 + G ++ GQVC + R+F+H D D+ + + + E LR G KDT +GPL+ Sbjct: 253 EPIVKGGYYHAGQVCVSTQRIFVHDDIADDFTEALVARVERLRTGDPTLKDTDVGPLIQP 312 Query: 346 EQHERVLSYIQKGKDEGAKAVTGGSCPFEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTA 405 + +RV +I + GAK TGG E + PTV + + + +E+FGPV+ Sbjct: 313 READRVAEWIDEAVKGGAKLATGGKRLSET--TLQPTVLLDPASDARVTTQEVFGPVVAV 370 Query: 406 IPYETVDEVIERANHSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAA-SPFG 464 Y +DE I RAN A ++T+++ A A+RL A V +N F PF Sbjct: 371 YRYADLDEAISRANSLPTAFQASIFTQDIDIALRAANRLDASAVMINDATAFRTDWMPFA 430 Query: 465 GYKQSGLGREMGSYALDNYTEVKSV 489 G ++SG G Y + + ++ K + Sbjct: 431 GRRESGYGTGGIPYTMRDMSQEKMI 455 Lambda K H 0.316 0.133 0.391 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: 455 Number of extensions: 29 Number of successful extensions: 5 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: 495 Length of database: 460 Length adjustment: 33 Effective length of query: 462 Effective length of database: 427 Effective search space: 197274 Effective search space used: 197274 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: 51 (24.3 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