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_101588547.1 BJEO58_RS05920 thiolase family protein

Query= BRENDA::Q0K368
         (391 letters)



>NCBI__GCF_900169175.1:WP_101588547.1
          Length = 388

 Score =  401 bits (1030), Expect = e-116
 Identities = 214/390 (54%), Positives = 269/390 (68%), Gaps = 6/390 (1%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           M EA IV A RTA GR+GG L   HP DL A VL  LVER G DPAL+EDV+ GCV+QVG
Sbjct: 1   MPEAVIVDAARTAVGRRGGALRDVHPVDLGAHVLRGLVERNGLDPALIEDVVFGCVTQVG 60

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
           EQ  NV R A LA+  PE+V GT+VDR CGSSQQAL FA  +V++G  DIVIA GVESMT
Sbjct: 61  EQGSNVGRWAALAAGFPETVAGTTVDRACGSSQQALTFAVASVIAGHSDIVIAGGVESMT 120

Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
           RVPMG        NG G    P +E RY    FSQ  GAEM+A +++L+R QLD  AL+S
Sbjct: 121 RVPMGSQRN----NGPGKAFGPAVEERYGRDSFSQGEGAEMVAERWNLTRTQLDELALES 176

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLI-AEGGR 239
           H RA+AAT++G  + +ILP+  +T +G   +    DEG+R   TLE +G++  +  E G 
Sbjct: 177 HARALAATEAGVLSEQILPIAGQTKEGETQDFRR-DEGIRPGGTLEKLGTLPTVFKEDGV 235

Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299
           VTA ++SQI DGA+ L+V+     ++LG+ P+ARVH   +   DPV+ML AP+PATE AL
Sbjct: 236 VTAGNSSQISDGASALLVMTPERARELGLTPIARVHTAALAATDPVIMLTAPIPATEKAL 295

Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359
           KK+GL   DI +FEVNEAFA VPLAW++  G    R+N +GGAIA GHPLG SGA++MT 
Sbjct: 296 KKSGLSPADIGVFEVNEAFASVPLAWMQEFGVGADRVNPNGGAIAFGHPLGASGARIMTD 355

Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVE 389
           L+H +   G +YGLQTMCE GG AN TI+E
Sbjct: 356 LIHTMRATGTQYGLQTMCEAGGQANATILE 385


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: 456
Number of extensions: 15
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: 391
Length of database: 388
Length adjustment: 30
Effective length of query: 361
Effective length of database: 358
Effective search space:   129238
Effective search space used:   129238
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