GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Dinoroseobacter shibae DFL-12

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 3607419 Dshi_0833 AMP-dependent synthetase and ligase (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>lcl|FitnessBrowser__Dino:3607419 Dshi_0833 AMP-dependent synthetase
           and ligase (RefSeq)
          Length = 541

 Score =  196 bits (498), Expect = 2e-54
 Identities = 169/537 (31%), Positives = 241/537 (44%), Gaps = 43/537 (8%)

Query: 43  PEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATA 102
           P+REA+V  +  RR+TYA+      RLASAL G G+ PGD V     N    V       
Sbjct: 34  PDREAVV--YGARRFTYAEYHARVSRLASALAGAGIAPGDVVATLLPNIPAMVEAHFGVP 91

Query: 103 QVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHL 162
             G VL  IN       V Y L+  G K ++       S +L +  E      G  P  +
Sbjct: 92  ACGAVLNTINIRLDVDTVAYILSHGGAKAVLV-----DSQFLPLAAEACERLDGPAPLLI 146

Query: 163 QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQ 222
           + A           DD AG  A   G   + + +A G+   P +          + + + 
Sbjct: 147 EVA-----------DDAAGVHA-LGGYTEYEDFLAGGDPDFPWIMP----RDEWESLALN 190

Query: 223 FTSGTTGFPKGATLTHRN--ILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACF 280
           +TSGTTG PKG    HR   ++  G  I   M L P  R    VPL+HC G     +   
Sbjct: 191 YTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVLYP--RWLAIVPLFHCNGWNHSWMMPM 248

Query: 281 THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMA 340
             G T+V   D      +   + +   T   G P +    ++ P  A    S       A
Sbjct: 249 L-GGTVVCCRD-VSAQAIYTAIAENGVTHFGGAPIVLNMIVNAPDAARRPFSHTVEVFTA 306

Query: 341 GSPCPTEVMKRVVEQMNLREITIAYGMTET--SPVSCQSSTD---TPLSKRVSTV---GQ 392
           G+P P       +E++    +T  YG+TET      C  + D    P ++R +     G 
Sbjct: 307 GAP-PAAATLAAIEELGFN-VTQVYGLTETYGHVTECVWNPDWDTLPQAERAAIKARQGV 364

Query: 393 VQPHLE-VKIVDPDTGAVVPIGQR-GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGD 450
             P +E + ++DP+   V   G   GE   +G SVM GY+ +   T EA   GG+ H+GD
Sbjct: 365 ALPQMEHITVMDPEMRQVPMDGATTGEVMMRGNSVMKGYYRNPDATAEAF-AGGYFHSGD 423

Query: 451 LATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELC 510
           +A    +GY+ I  R KD++I GGENI   E+E  L  HP V    VV  PD  +GE  C
Sbjct: 424 IALQHPDGYIQIADRAKDIIISGGENISSVEVEGALMHHPAVLLCAVVAKPDPTWGEVPC 483

Query: 511 AWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567
           A++  K G    E +I AF + ++A +K P+ + F T  P T TGKIQKF++R+  K
Sbjct: 484 AFVELKDGKTAEEAEIIAFARERLAGFKTPKKVVF-TELPKTSTGKIQKFELRNRAK 539


Lambda     K      H
   0.320    0.136    0.412 

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: 729
Number of extensions: 41
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: 578
Length of database: 541
Length adjustment: 36
Effective length of query: 542
Effective length of database: 505
Effective search space:   273710
Effective search space used:   273710
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: 53 (25.0 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 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