GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Brevibacterium jeotgali SJ5-8

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101587838.1 BJEO58_RS03590 thiolase family protein

Query= BRENDA::Q0K368
         (391 letters)



>NCBI__GCF_900169175.1:WP_101587838.1
          Length = 393

 Score =  338 bits (868), Expect = 1e-97
 Identities = 184/392 (46%), Positives = 254/392 (64%), Gaps = 8/392 (2%)

Query: 3   EAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVGEQ 62
           +A IV AVRT  G++GG L   HP DL A  +  LVER+G D  L++D I+G   Q GEQ
Sbjct: 7   QAVIVDAVRTPVGKRGGALREHHPVDLMATTIGHLVERSGVDQELLDDAIVGVGLQRGEQ 66

Query: 63  AGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMTRV 122
            GNVARNA+L + LP ++PGT++DRQCGS QQA+ FAAQAV +G     +A GVESM+R 
Sbjct: 67  TGNVARNAVLGAGLPVALPGTTIDRQCGSGQQAVQFAAQAVRAGDYRFALAGGVESMSRT 126

Query: 123 PMG--LSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
            +G       P    +G        AR+ G   SQ    +++ ++Y  +RE++DA+A++S
Sbjct: 127 DLGPLFDPAGPQGEWYGTQAL----ARFDGDLPSQGRSIDLVVKEYGFTREEMDAFAIRS 182

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK-LIAEGGR 239
           H RA AAT++GRFT +++P+   T DGA   + T DEG+R       + S+  + +  G+
Sbjct: 183 HHRAAAATEAGRFTHDLVPLNGLTKDGAEVAL-TADEGIRPSVDPAKVASLAPVFSPDGK 241

Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299
           VTA ++SQI DGAA L++ +    +  G++P AR+ A      DPV+   A LPA+ +AL
Sbjct: 242 VTAGNSSQISDGAAALLIADRDAAESAGLRPRARIVASVARAADPVLQFTAILPASHLAL 301

Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359
            KAGL IGD+DL EVNEAFAPVPL + +  G     LNV+GG+IA+GHP+G +GA+L+T 
Sbjct: 302 AKAGLTIGDMDLIEVNEAFAPVPLLFQREFGVSDDILNVNGGSIAIGHPIGSTGARLLTG 361

Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           LV  L     RYGL T+CEGGG+AN TI+ERL
Sbjct: 362 LVSELERRDARYGLLTICEGGGMANATIIERL 393


Lambda     K      H
   0.317    0.132    0.379 

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: 476
Number of extensions: 21
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: 391
Length of database: 393
Length adjustment: 31
Effective length of query: 360
Effective length of database: 362
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 (21.7 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