GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Cupriavidus basilensis 4G11

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate RR42_RS07610 RR42_RS07610 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__Cup4G11:RR42_RS07610
          Length = 393

 Score =  711 bits (1836), Expect = 0.0
 Identities = 361/393 (91%), Positives = 377/393 (95%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           MTD+VIVSAARTAVGKFGGSLAKIPAPELGA+VIKAALERAGVKPEQVSEVIMGQVLTAG
Sbjct: 1   MTDIVIVSAARTAVGKFGGSLAKIPAPELGAIVIKAALERAGVKPEQVSEVIMGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
           SGQNPARQAA+KAGLP MVPAMTINKVCGSGLKAVMLAANAI AGDAEIVVAGGQENMSA
Sbjct: 61  SGQNPARQAALKAGLPVMVPAMTINKVCGSGLKAVMLAANAIAAGDAEIVVAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           APHVLPGSRDGFRMGDAKL+D+MIVDGLWDVYNQYHMG+TAENVAKEYGITREAQD FA 
Sbjct: 121 APHVLPGSRDGFRMGDAKLIDSMIVDGLWDVYNQYHMGVTAENVAKEYGITREAQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
           GSQNKAEAAQKAGKFDEEIVPV IPQRKGDPV F TDEFVR G T D+++GLKPAFDKAG
Sbjct: 181 GSQNKAEAAQKAGKFDEEIVPVPIPQRKGDPVMFATDEFVRHGVTQDALAGLKPAFDKAG 240

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTAANASGLNDGAAAVVVMSAAKAKELGLTPLATI++Y  AGVDPKVMGMGPVPASKR 
Sbjct: 241 SVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIRAYGTAGVDPKVMGMGPVPASKRC 300

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           LSRA W+ ++LDLMEINEAFAAQALAVH+QMGWDTSKVNVNGGAIAIGHPIGASGCRILV
Sbjct: 301 LSRAGWSVEELDLMEINEAFAAQALAVHKQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVERK 393
           TLLHEMKRRDA KGLASLCIGGGMGVALAVERK
Sbjct: 361 TLLHEMKRRDAHKGLASLCIGGGMGVALAVERK 393


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: 646
Number of extensions: 24
Number of successful extensions: 1
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 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