GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sinorhizobium meliloti 1021

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__Smeli:SM_b20589
          Length = 400

 Score =  337 bits (864), Expect = 4e-97
 Identities = 183/400 (45%), Positives = 260/400 (65%), Gaps = 11/400 (2%)

Query: 3   REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61
           RE  +    RTP+G FGG+L  V +  LGAI +   + R   +  E +D+VIFGC  QAG
Sbjct: 2   REAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQAG 61

Query: 62  L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120
              +N+AR  ++ AG+P  V   TIN++CGSG+ AV  AA+ IK G+A++++AGG E+M 
Sbjct: 62  EDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESMS 121

Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMV-WGGLTDVFNGYH----MGITAENINDMYGITR 175
           +APF+LP A   +  +    ++ D  + W  +  +    +    M  T EN+ + Y ++R
Sbjct: 122 RAPFVLPKAESAFSRN---AEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDYKVSR 178

Query: 176 EEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTPEAMAKLA 234
           E+QDAF  RSQ  AA A  +GR   EIV V I  +KG  +V D DEHPR +T EA+A L 
Sbjct: 179 EDQDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRDEHPRATTIEALAGLK 238

Query: 235 PAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGP 294
             F++GG+VTAGNASG+ND AAA+I+ S+E A + G++PMA+++  AS GV P +MG+GP
Sbjct: 239 TPFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGMGP 298

Query: 295 IPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPI 354
           +PAS++ + + G T D  D+IE NEAFA+Q +AV R LG AD   +VN NGGAIA+GHP+
Sbjct: 299 VPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPL 358

Query: 355 GSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           G SGARI  T   E+ + G +  L+T+CIG G G A+ +E
Sbjct: 359 GMSGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALE 398


Lambda     K      H
   0.317    0.135    0.387 

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: 461
Number of extensions: 21
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: 396
Length of database: 400
Length adjustment: 31
Effective length of query: 365
Effective length of database: 369
Effective search space:   134685
Effective search space used:   134685
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 (21.7 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