GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dadA in Acidovorax sp. GW101-3H11

Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ac3H11_1644 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)

Query= reanno::azobra:AZOBR_RS08020
         (436 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1644
          Length = 405

 Score =  236 bits (601), Expect = 1e-66
 Identities = 142/402 (35%), Positives = 202/402 (50%), Gaps = 4/402 (0%)

Query: 1   MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60
           M+V VLG+G++G++TAY L + G +VTV+D Q  P    S  N  ++S  Y  P A   L
Sbjct: 1   MQVCVLGAGIVGLATAYELHQRGMQVTVID-QAQPGTGASGGNGAQLSYSYVQPLANADL 59

Query: 61  MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120
             +  + +L   SPL +RP+ D   W W L+ L   N R+ E +  +++ LA  SR    
Sbjct: 60  WQQLPELLLSPRSPLKMRPQWDVHQWRWGLEFLRACNRRTSERSTEQLLALATLSRHGFE 119

Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180
            +R    +  D  + G L ++ T   + AA   M +   +      +  + C  +EPAL+
Sbjct: 120 AMRQAEQLDCDFSSTGKLVLYSTPAGLAAAQRQMELQRAWGSEQESVSPQRCVEIEPALQ 179

Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTD 240
             +  I G +  P +   DC      L  +    GV F     I       +R+  V T 
Sbjct: 180 HYQSHIAGAIHTPSECAADCLAVCQGLHRILAARGVHFVLGARIEGFVRRAQRIAAVQTS 239

Query: 241 AGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAA-GAPESTVMDETHK 299
           AG + A  +V+A+GS S    +  G  LPVYP+KGYS+TL   DAA  AP   V D   K
Sbjct: 240 AGAIEAQQFVLALGSASHQAAQTLGFRLPVYPLKGYSITLDTTDAANAAPRVNVTDAARK 299

Query: 300 IAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAEFWTGLRPNT 359
           +   R+G R+RV G AEL G +  + P R   L      LFP   D  +   WTG+RP T
Sbjct: 300 VVFARIGQRLRVAGMAELVGHNHHIPPARIQSLREATRALFPGCSDFGELRPWTGMRPAT 359

Query: 360 PDGTPIVG--PTPVRNLFLNTGHGTLGWTMAAGSGRVVADVV 399
           P G P+VG  P    NL LNTGHG LG+T+A G+   VA++V
Sbjct: 360 PTGVPLVGRHPHAPDNLLLNTGHGALGFTLAFGTAAQVAELV 401


Lambda     K      H
   0.319    0.136    0.408 

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: 395
Number of extensions: 17
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: 436
Length of database: 405
Length adjustment: 32
Effective length of query: 404
Effective length of database: 373
Effective search space:   150692
Effective search space used:   150692
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 (21.7 bits)
S2: 50 (23.9 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