Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_052591396.1 VV02_RS10095 aldehyde dehydrogenase family protein
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001190945.1:WP_052591396.1 Length = 485 Score = 432 bits (1110), Expect = e-125 Identities = 228/469 (48%), Positives = 309/469 (65%), Gaps = 9/469 (1%) Query: 16 LQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEW 75 LQ + L+I+G+FV +G++F T NPAT E L + EA A DVDKAVKAAR A+ + W Sbjct: 18 LQSSYGLFINGEFV-DGTGSSFKTINPATEEKLADVSEASADDVDKAVKAARTAYTR-VW 75 Query: 76 RTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWC 135 MS A R + ++++A +M+E ELA LE+LDNGKPI E+ + D+P A H Y+AGW Sbjct: 76 SRMSGAERGKYVFRIARIMQERARELAVLESLDNGKPIKESRDVDVPTAAAHFFYHAGWA 135 Query: 136 TKITGQTIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQ 195 K+ + +G+ P+GVVGQ+IPWNFPLLM WK+ ALATG T+VLKPAE Sbjct: 136 DKLEYAGLSPAGS----PPPRPLGVVGQVIPWNFPLLMLAWKIAPALATGNTVVLKPAET 191 Query: 196 TPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMST 255 TPL+AL AE+ QA P GV+NI+ G G G+AL H VDKIAFTGST++GK I + Sbjct: 192 TPLTALLFAEICQQADLPPGVVNIVTGAGA-TGQALVEHPDVDKIAFTGSTDVGKAIARS 250 Query: 256 AAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDE 315 A + KR TLELGGK+ NI+ DA + +A+ G +NG+ FNQG VCCAGSR+ + + DE Sbjct: 251 IAGTRKRATLELGGKAANIVFEDAAIDQAVEGIVNGIFFNQGHVCCAGSRLLVQESVADE 310 Query: 316 VVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFEA 375 VV + ++LR G L K+T +G + SK Q +R+ + G+ EGA T C A Sbjct: 311 VVRRLERRMKTLRVGDPLDKNTDVGAINSKAQLQRITELVDAGEAEGATRWT-VPCELPA 369 Query: 376 -GYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENV 434 G++ APTVF +V +A EEIFGPVL+ + + T E + +AN++ YGL+AG+WTE Sbjct: 370 RGFWFAPTVFTDVSQTHRVATEEIFGPVLSVLTFRTPQEAVAKANNTPYGLSAGIWTEKG 429 Query: 435 KQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNY 483 + ++AD+L+AG VW N +N FD SPFGGYK+SG GRE G + L+ Y Sbjct: 430 SRILWMADQLKAGVVWANTFNRFDPTSPFGGYKESGYGREGGRHGLEAY 478 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: 636 Number of extensions: 26 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: 495 Length of database: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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 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