GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Klebsiella michiganensis M5al

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate BWI76_RS13135 BWI76_RS13135 3-oxoadipyl-CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS13135 BWI76_RS13135
           3-oxoadipyl-CoA thiolase
          Length = 401

 Score =  331 bits (849), Expect = 2e-95
 Identities = 184/402 (45%), Positives = 260/402 (64%), Gaps = 14/402 (3%)

Query: 3   REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61
           R+  +    RTP+G +GG L  + +  L AI + E + R        ID+VI GC  QAG
Sbjct: 2   RDAFICDGIRTPIGRYGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQAG 61

Query: 62  L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120
              +NVA    + AG P  V   T+N++CGSGL A+  AA+ IKAG+AD+++AGG E+M 
Sbjct: 62  EDNRNVAHMATLLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVESMS 121

Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMV-WGGLTDV----FNGYHMGITAENINDMYGITR 175
           +APF++  A   Y+    + +L D  + W  +  +    F    M  TAEN+ ++  I+R
Sbjct: 122 RAPFVMGKASAAYQR---QAELFDTTIGWRFVNPLMQQRFGTDSMPETAENVAELLNISR 178

Query: 176 EEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI--VFDTDEHPR-KSTPEAMAK 232
            +QDAF +RSQ  +A+A   G    EIVPV I G KG +  V++ DEHPR ++T E +++
Sbjct: 179 ADQDAFAYRSQQRSARAQRDGILAQEIVPVPIIGGKGAVSTVYE-DEHPRAETTLEQLSR 237

Query: 233 LAPAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGL 292
           L   F+KGG VTAGNASG+ND AAA+I+ S ++A   G+ P A++V+ A+ GV+P +MGL
Sbjct: 238 LKTPFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAMATAGVEPKLMGL 297

Query: 293 GPIPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGH 352
           GP+PA RK LE+AGL+I D+DLIE NEAFAAQ++ V R LG AD    VN NGGAIA+GH
Sbjct: 298 GPVPAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNPNGGAIALGH 357

Query: 353 PIGSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           P+G SGAR+ ++   E+Q+R  +  L T+CIG G G A+I+E
Sbjct: 358 PLGMSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILE 399


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: 448
Number of extensions: 18
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: 401
Length adjustment: 31
Effective length of query: 365
Effective length of database: 370
Effective search space:   135050
Effective search space used:   135050
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 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