GapMind for catabolism of small carbon sources

 

Alignments 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_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__Koxy:BWI76_RS16135
          Length = 400

 Score =  329 bits (844), Expect = 7e-95
 Identities = 172/398 (43%), Positives = 256/398 (64%), Gaps = 9/398 (2%)

Query: 4   EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62
           +  +  A RTP G FGGTL  + +  L A+ +   ++R  G+   +ID+VI+GC  QAG 
Sbjct: 3   QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGE 62

Query: 63  -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121
             +NVAR  ++ AG+P+ V   T+N++CGS L A+ +AA+ IK+G+  +++AGG E+M +
Sbjct: 63  DNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSR 122

Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177
           APF++  A   +  +M   D    + W  +       +    M  TAEN+ D + I+R +
Sbjct: 123 APFVMGKAESAFSRTMRMEDTT--IGWRFINPQMKALYGVDSMPETAENVADDFAISRAD 180

Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTPEAMAKLAPA 236
           QDAF  RSQ   A A E+GRF DE++ V +  +KG+ ++F  DEHPR +T EA+A+L   
Sbjct: 181 QDAFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPRTTTAEALARLRGV 240

Query: 237 FKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIP 296
            +  G+VTAGNASG+ND A A+++ S++      ++P+A+VV  A+ GV P +MG GP P
Sbjct: 241 VRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPAP 300

Query: 297 ASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGS 356
           A RK L + GLT+  +D+IE NEAFAAQ++AV RDLG  D    VN NGGAIA+GHP+G+
Sbjct: 301 AVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLGA 360

Query: 357 SGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           SG R+ +T  Y++++ G +  L T+CIG G G ALI+E
Sbjct: 361 SGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIE 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: 447
Number of extensions: 23
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