GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kauB in Dyella japonica UNC79MFTsu3.2

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4224 N515DRAFT_4224
           coniferyl-aldehyde dehydrogenase
          Length = 456

 Score =  145 bits (365), Expect = 4e-39
 Identities = 108/343 (31%), Positives = 165/343 (48%), Gaps = 14/343 (4%)

Query: 156 EPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAELAVEAGIPKG 215
           +P+GVVG IVPWN+PL +A   +  AL+ GN V++K SE +P  +   A+LA     P+ 
Sbjct: 94  QPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYTPQFSALFAQLAARYFKPEE 153

Query: 216 VLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESNMKRVWLEAGGKSPNI 275
           V  V+ G         AL    D L+FTGST + + ++  +  +N+  V LE GGKSP I
Sbjct: 154 VC-VVTGDADVAQAFSAL--PFDHLLFTGSTAVGRHVM-RAASANLTPVTLELGGKSPAI 209

Query: 276 VFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKAWKPGNPL 335
           V   A    +A E       FN G+ C A   +L+ R+  D+F+    +      P    
Sbjct: 210 VGPGA-RFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAAARDVAARLYP---- 264

Query: 336 DPATN--VGALVDTQQMNTVLSYIESGHADGARLVAGGKRTLQETGGTYVEPTIFDGVSN 393
            P  N    +++  +Q   + +  +    DGA+L   G  T  +     + P +  GVS 
Sbjct: 265 QPVRNEQYASIISERQYQRLAALRDDAARDGAKLTLLGDET-DDIQRRRMTPALLTGVSE 323

Query: 394 AMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADISKAHLTARALRAGSV 453
           +M + QEEIFGP+L ++ +D  E+AIA     P+ LA  ++  D +          AG V
Sbjct: 324 SMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGALVDRVLARTTAGGV 383

Query: 454 WVNQ--YDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATW 494
            +N   Y       PFGG   SG+G       F  ++ LK+ +
Sbjct: 384 TINDTLYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLKSVF 426


Lambda     K      H
   0.316    0.132    0.390 

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: 520
Number of extensions: 27
Number of successful extensions: 6
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: 497
Length of database: 456
Length adjustment: 33
Effective length of query: 464
Effective length of database: 423
Effective search space:   196272
Effective search space used:   196272
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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