Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28685 Length = 496 Score = 503 bits (1294), Expect = e-147 Identities = 252/494 (51%), Positives = 339/494 (68%), Gaps = 8/494 (1%) Query: 6 MQVTKRLETFLQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKA 65 +Q+ +E FL +L+I G + +A+G F NPAT TL + E DVD AV A Sbjct: 4 IQLLPAVEKFLSQPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAA 63 Query: 66 ARKAFDQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAI 125 AR AF G W SPA R L+++LA+L+++H+ ELAQL TL+NGKPI G+ A Sbjct: 64 ARAAFT-GTWAQQSPAQRGLLLFRLAELLDQHREELAQLITLENGKPIG-AARGEAASAA 121 Query: 126 EHMRYYAGWCTKITGQTIPVSGA----YFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAA 181 +RY+AGW TKI G T+PVS + NYT EPVGV I+PWNFPL M +WK+G Sbjct: 122 NIIRYFAGWPTKIEGSTLPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPV 181 Query: 182 LATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIA 241 LATGC VLKPAEQTPL A+ L +LI+ AGFPAGV+N++ G G G L H VDKIA Sbjct: 182 LATGCVAVLKPAEQTPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDVDKIA 241 Query: 242 FTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCC 301 FTGST++G+ I A ++K+V+LELGGKSPNI+LPDA++ +A GA +G+ +NQGQVC Sbjct: 242 FTGSTQVGRLIAQAATGNMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQGQVCT 301 Query: 302 AGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDE 361 AGSR+++H D+V++E+ +A + G GL + +GPLVS Q V Y+Q+G++E Sbjct: 302 AGSRLYVHASVLDQVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEE 361 Query: 362 GAKAVTGGSCP--FEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERAN 419 GA+ + GG P E G+F+ P+VF + + +A+EEIFGPVLT + + +DE++ RAN Sbjct: 362 GAELICGGDRPAHLERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRAN 421 Query: 420 HSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYA 479 S YGLAAGLWT +++ AH +A +L+AG+VW+NC+NV D ASPFGGYKQSG GREMG Sbjct: 422 DSPYGLAAGLWTRDLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNV 481 Query: 480 LDNYTEVKSVWVNL 493 +D YTE KSV+V+L Sbjct: 482 IDAYTETKSVYVDL 495 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: 686 Number of extensions: 21 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: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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: 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