GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sphingopyxis indica DS15

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_089215596.1 CHB69_RS08555 acetyl-CoA C-acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_900188185.1:WP_089215596.1
          Length = 404

 Score =  317 bits (812), Expect = 4e-91
 Identities = 187/400 (46%), Positives = 252/400 (63%), Gaps = 18/400 (4%)

Query: 6   IVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAGSGQNP 65
           IV+  RTAVGKFGG+L+ + A ELGAV++KA +ER  + P +V +V+  Q    G+G+ P
Sbjct: 8   IVAPIRTAVGKFGGTLSPLTAGELGAVILKALVERTKIDPARVDDVVFSQ--GYGNGEAP 65

Query: 66  A--RQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSAAPH 123
           A    + + AGLP  VP   +++ CGSGL+AV+ AA  +  G +++VVAGG E+MS   H
Sbjct: 66  AIGHWSWLAAGLPLEVPGYQLDRRCGSGLQAVVNAAMMVQTGMSDVVVAGGVESMSNVEH 125

Query: 124 VLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGI------TAENVAKEYGITREAQDE 177
                R G R G+  L D +    L     +   G+      TAEN+AK+YGITREA D 
Sbjct: 126 YSTDIRKGVRAGNLTLHDRLTRGRLMSQPIE-RFGVISGMIETAENLAKDYGITREAADA 184

Query: 178 FAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFD 237
           +AV S  +A AA   G F++E+VPV +PQRKGDP+ F  DE  R  AT++S+  L+    
Sbjct: 185 YAVRSHQRAAAAWDKGLFNDELVPVSVPQRKGDPIVFDHDEGYRADATMESLGKLRAL-- 242

Query: 238 KAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPAS 297
           + G VTA NAS  ND AAA +V++  K +ELGL P+A   S A AG DP  MG+GPVPA 
Sbjct: 243 EGGVVTAGNASQQNDAAAACLVVAEDKLEELGLEPIAWYHSSAAAGCDPSRMGIGPVPAV 302

Query: 298 KRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGW--DTSK---VNVNGGAIAIGHPIG 352
           +R  +R      D+DL+E+NEAFA Q LAV +  GW  D S+   +NVNG  I++GHPIG
Sbjct: 303 ERLFARNGLGWGDIDLVELNEAFAPQVLAVLKGWGWSDDDSRGDILNVNGSGISLGHPIG 362

Query: 353 ASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           A+G RIL  L  E+ RRD + GL ++CIGGG G+A   ER
Sbjct: 363 ATGGRILANLTRELVRRDGRYGLETMCIGGGQGIAAIFER 402


Lambda     K      H
   0.315    0.131    0.369 

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: 415
Number of extensions: 17
Number of successful extensions: 4
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: 393
Length of database: 404
Length adjustment: 31
Effective length of query: 362
Effective length of database: 373
Effective search space:   135026
Effective search space used:   135026
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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