GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Magnetospirillum magneticum AMB-1

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_011384976.1 AMB_RS13060 acetyl-CoA C-acyltransferase

Query= SwissProt::Q0AVM3
         (396 letters)



>NCBI__GCF_000009985.1:WP_011384976.1
          Length = 398

 Score =  304 bits (779), Expect = 3e-87
 Identities = 173/398 (43%), Positives = 240/398 (60%), Gaps = 27/398 (6%)

Query: 12  RTPVGTFGGTLKDVGSAQLGAIVMGEAIKRAGIKAEQIDEVIFGCVLQAGL-GQNVARQC 70
           R+P+G  GG L  V S  L A V+   + R+  K E +++VI GC  QAG   +NVAR  
Sbjct: 11  RSPIGRHGGGLAPVRSDDLAAEVIRALVARSSFKPEDVEDVILGCTNQAGEDSRNVARHA 70

Query: 71  MINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKAPFILP--N 128
            + AG+P EV   T+N++C SGL AV  AA+ +  G+ D+ +AGG E+M +APF+L   +
Sbjct: 71  ALLAGLPVEVAGQTVNRLCASGLAAVLDAARSVTCGEGDLYLAGGVESMTRAPFVLAKGD 130

Query: 129 ARW-----------GYRMSMPKGDLIDEMVWGGLTDVFNGYHMGITAENINDMYGITREE 177
           + W           G R + PK           +   F G+ M  TA+NI    G++RE 
Sbjct: 131 SAWSRDARIFDTTIGARFANPK-----------VVKSFGGHSMPETADNIAHDLGLSREA 179

Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIVFDTDEHPRKSTP-EAMAKLAPA 236
            DAF   SQ   A+A   G ++ EI P+ I G+KGD +   DEHPR  T   A+ KL P 
Sbjct: 180 SDAFAAASQAKYAKAKAEGFYEGEIHPITIAGRKGDTIVAEDEHPRPQTDLAALTKLKPL 239

Query: 237 FKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIP 296
           F+ GG VTAGNASGIND AAA+ + S+   ++ GI P+A++V+ A+ GV P VMGLGP+P
Sbjct: 240 FE-GGVVTAGNASGINDGAAALFIGSRAAGEKAGIAPIARIVAGAAAGVPPRVMGLGPVP 298

Query: 297 ASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGS 356
           A  KAL +A L++ D+DLIE NEAFA Q +     LG A    ++N NGGAIAIGHP+G 
Sbjct: 299 AITKALARAKLSLKDLDLIEINEAFAVQVLGCVTQLGVAADDSRLNPNGGAIAIGHPLGC 358

Query: 357 SGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           SGAR+ +T   ++Q+ G +  + +LCIG G G A ++E
Sbjct: 359 SGARLALTAARQLQRTGGRHAVVSLCIGVGHGLAAVIE 396


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: 460
Number of extensions: 18
Number of successful extensions: 3
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: 398
Length adjustment: 31
Effective length of query: 365
Effective length of database: 367
Effective search space:   133955
Effective search space used:   133955
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