GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxD in Pseudomonas putida KT2440

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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