GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3607419
          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:

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