Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized)
to candidate PP_0708 PP_0708 putative Betaine-aldehyde dehydrogenase
Query= SwissProt::Q84HH8 (515 letters) >FitnessBrowser__Putida:PP_0708 Length = 476 Score = 145 bits (365), Expect = 4e-39 Identities = 137/440 (31%), Positives = 205/440 (46%), Gaps = 30/440 (6%) Query: 1 MKLANYVYGQWIEGAGEGA-ALTDPVTGEALVRVSSDGID-VARALEFARTAGGAALKAL 58 M ++Y+ G W+EG G ++ DP G+ + + + V +A+ AR+A A K+ Sbjct: 1 MTTSHYIAGHWVEGQGSDCISVNDPALGQPFAELMAASVSQVDQAVAAARSAL-PAWKST 59 Query: 59 TYEERAAKLAAIAELLQAKRAEYFDISLRNSGATEGDASFDVDGAIFTVKSYARAGKALG 118 ERAA L AE L +R + +RN+G +A D+D AI T YA + L Sbjct: 60 CASERAAFLRGFAEQLGQRREALVTVQMRNNGKPRHEAEIDLDDAIATFGYYAELAEQLP 119 Query: 119 AGRHLKEGGRVALAKTDVFQGQHFLMPLTGVAVFINAFNFPAWGLWEKAAPALLAGVPVF 178 + + V LA F + L P+ GV I +NFP K APAL AG V Sbjct: 120 S-----KNRTVPLAAPG-FTARTRLEPV-GVVGLIVPWNFPLVTSAWKLAPALAAGCTVV 172 Query: 179 AKPATPTAWLAQRMVADVVEAGILPPGAISIVCGGARD--LLDHVTECDVVSFTGSADTA 236 KP+ T L ++ + +A LP G ++IV G A L + D +SFTGS Sbjct: 173 LKPSEVTP-LIEQAYGQIADALGLPAGVLNIVNGKAETGAALSNHNGLDKLSFTGSNSVG 231 Query: 237 ARMRTHPNVVARSVRINIEADSVNSAILGPDAQPGTPEFDLAVKEIVREMTVKTGQKCTA 296 +++ + R V + + S + ++ D + D AV+ IV ++ GQ C+A Sbjct: 232 SQVMRSASAQCRPVTLELGGKS--AIVVFDDC-----DVDQAVEWIVAGISWNAGQMCSA 284 Query: 297 IRRILAPAGVSRALADAVSGKLAGCKVGNPRSEGVRVGPLVSKAQQAAAFEGLAKLRQE- 355 R+L G++ AL + L +VGNP +E V +GPL S+AQ A R+E Sbjct: 285 TSRLLVQDGIADALLPRLQAALENLRVGNPLTEEVDMGPLTSQAQWLKVASYFATAREEG 344 Query: 356 CEVVFGGDPDFEPVDADAAVSAFVQPTLLYCDKGLAARHVHDVEVFGPVATMVPYADTRD 415 + + GG +D + FV PT LY D +R + E+FGPV +A Sbjct: 345 LQCLAGG----HALDRE---GWFVSPT-LYTDVPKDSR-LWTEEIFGPVLCARRFATEEQ 395 Query: 416 AVAIARRGHGSLVASVYSGD 435 A+A A LVA+V S D Sbjct: 396 AIAEANDSRFGLVATVCSAD 415 Lambda K H 0.319 0.135 0.399 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: 554 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: 515 Length of database: 476 Length adjustment: 34 Effective length of query: 481 Effective length of database: 442 Effective search space: 212602 Effective search space used: 212602 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