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_RS26090 RR42_RS26090 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__Cup4G11:RR42_RS26090
          Length = 391

 Score =  600 bits (1547), Expect = e-176
 Identities = 304/392 (77%), Positives = 340/392 (86%), Gaps = 1/392 (0%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M DVVIV+AARTAVGKFGGSLAK+PAPELGA VIKA LER+G+KPE V EV++GQVLTAG
Sbjct: 1   MEDVVIVAAARTAVGKFGGSLAKVPAPELGATVIKALLERSGLKPEMVDEVLLGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQAAIKAGLP  VPAMTI KVCGSGLKAV LAA AI  GDA+IV+AGGQENMSA
Sbjct: 61  GGQNPARQAAIKAGLPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           +PHVL GSRDG RMGD KL DTMIVDGLWD +NQYHMG TAENVAK Y I+RE QD FA 
Sbjct: 121 SPHVLAGSRDGQRMGDWKLTDTMIVDGLWDAFNQYHMGTTAENVAKAYHISREQQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQ KAE AQK G+F +EIVPV I  +KG  V F TDEF++ G T D+++GL+PAFDKAG
Sbjct: 181 ASQQKAELAQKTGRFKDEIVPVSIVSKKG-TVVFDTDEFIKHGTTADALAGLRPAFDKAG 239

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           +VTA NASGLNDGAAAV++MSA+KA+ELGLTPLA I SYA+AG+DP +MGMGPVPAS+R 
Sbjct: 240 SVTAGNASGLNDGAAAVLMMSASKARELGLTPLARIASYASAGLDPAIMGMGPVPASQRC 299

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L +A W+  DLDLMEINEAFAAQA AV+Q+M WD SK+NVNGGAIAIGHPIGASGCRILV
Sbjct: 300 LHKAGWSINDLDLMEINEAFAAQACAVNQEMDWDASKINVNGGAIAIGHPIGASGCRILV 359

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM RRDA++GLASLCIGGGMGVALAVER
Sbjct: 360 TLLHEMARRDARRGLASLCIGGGMGVALAVER 391


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: 552
Number of extensions: 18
Number of successful extensions: 2
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: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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