GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsB in Paraburkholderia bryophila 376MFSha3.1

Align LacI family transcriptional regulator (characterized, see rationale)
to candidate H281DRAFT_05225 H281DRAFT_05225 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= uniprot:A0A161ZH48
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_05225
          Length = 320

 Score =  462 bits (1188), Expect = e-135
 Identities = 237/313 (75%), Positives = 275/313 (87%), Gaps = 2/313 (0%)

Query: 8   RLLAVAMLAAASAALPVSSAFAETP--EKPKVALVMKSLANEFFLTMEDGAKAYQKDHSG 65
           R++A A+LA AS ALP S+A+A+     KPKVALVMKSLANEFFLTME GAK YQK +S 
Sbjct: 8   RIVAAAILATASTALPFSAAYAQNAPAHKPKVALVMKSLANEFFLTMETGAKDYQKHNSS 67

Query: 66  DFELISNGIKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGITVINI 125
            F+LI+NGIKDETDTA Q RIVEQMI+SKV+A+V+APADSKA+VPV+KKAVDAGI V+NI
Sbjct: 68  QFDLITNGIKDETDTANQIRIVEQMIVSKVDAIVLAPADSKALVPVVKKAVDAGIIVVNI 127

Query: 126 DNQLDPAVVKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTNAQQRT 185
           DN+LDP V+KSK++ VPFVGPDNRKGA+ VG+YLAK+LKAGDEVGIIEGVSTTTNAQQRT
Sbjct: 128 DNRLDPDVLKSKDLNVPFVGPDNRKGAQKVGDYLAKKLKAGDEVGIIEGVSTTTNAQQRT 187

Query: 186 AGFKDAMEAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGAVSAVR 245
           AGFKDAM+    KVVS+QSG+WEIDKG  VAS+ML+EYPN+KALLAGND+MA+GAVSAVR
Sbjct: 188 AGFKDAMQTVGAKVVSVQSGEWEIDKGNAVASAMLNEYPNLKALLAGNDNMAIGAVSAVR 247

Query: 246 AAGKAGKVQVVGYDNINAIKPMLKDGRVLATADQFAARQAVFGIETALKIIKGETVDSGA 305
           AAGK GKV VVGYDNINAIKPMLKDGRVLATADQ+AA+QAVFGI+TALK +      S  
Sbjct: 248 AAGKQGKVMVVGYDNINAIKPMLKDGRVLATADQYAAKQAVFGIDTALKALSEHKKQSQL 307

Query: 306 NGVIETPVELVTK 318
           +GV+ETP +LVTK
Sbjct: 308 SGVVETPCDLVTK 320


Lambda     K      H
   0.314    0.130    0.348 

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: 349
Number of extensions: 11
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: 318
Length of database: 320
Length adjustment: 28
Effective length of query: 290
Effective length of database: 292
Effective search space:    84680
Effective search space used:    84680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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