GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Burkholderia phytofirmans PsJN

Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS04180 BPHYT_RS04180 sugar ABC transporter substrate-binding protein

Query= uniprot:A0A165KPY4
         (416 letters)



>FitnessBrowser__BFirm:BPHYT_RS04180
          Length = 415

 Score =  410 bits (1055), Expect = e-119
 Identities = 218/411 (53%), Positives = 274/411 (66%), Gaps = 6/411 (1%)

Query: 7   IAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDS 66
           I A  +  +A ++++A  + VLH+WTSGGE+K++  LK  M  +G+ W+DFAVAGG G +
Sbjct: 10  IVASTLATSAQVASAAESLSVLHWWTSGGESKAIRVLKDDMDKQGYEWKDFAVAGGAGAA 69

Query: 67  AMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMKY 126
           AMT LK++V+SGN PSAAQ KGP IQ+WA +GVL ++D    A  W   LP  +   M  
Sbjct: 70  AMTALKTQVMSGNAPSAAQIKGPLIQDWADQGVLVDIDK--SATDWKAQLPAQINKTMMS 127

Query: 127 KGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQN 186
           KG YVAAP +VHR+NW+W +  AL K G    P TW EFFA ADK +AAG+ PVA GGQ 
Sbjct: 128 KGHYVAAPFSVHRINWLWINKAALDKVG-GKPPTTWPEFFALADKFRAAGITPVARGGQP 186

Query: 187 WQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDW 246
           WQD T +E+VVL  G A FY+ A++ LD   LTS  M +  +T R+I+GY D G+ GRDW
Sbjct: 187 WQDMTIWETVVLSQG-ADFYRKAMIDLDQKTLTSPQMLQVFQTARKIQGYFDKGSTGRDW 245

Query: 247 NLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKL 306
           NLATAM+I G  G Q MGDWAKGEF  A K    D++CAAAPG++NAFT+ VDSF+ F+ 
Sbjct: 246 NLATAMVINGSGGMQFMGDWAKGEFANANKKADVDYICAAAPGTSNAFTYTVDSFVFFQQ 305

Query: 307 K-DAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTAK 365
                A   Q  LA +IMSPAFQE F+L KGSIPVR    MDKFD CAK S  D   T K
Sbjct: 306 NGKKEATLGQLALAKTIMSPAFQEQFSLYKGSIPVRQDVSMDKFDACAKKSYADEQTTIK 365

Query: 366 SGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKTK 416
           S    PS A G   + ATEGAI DVV+ F N ++    +AM+K+AAAAK K
Sbjct: 366 SNTFFPSFAFGDVQSSATEGAITDVVTGFMNSNE-DPQEAMRKVAAAAKVK 415


Lambda     K      H
   0.315    0.128    0.383 

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: 564
Number of extensions: 32
Number of successful extensions: 5
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: 416
Length of database: 415
Length adjustment: 31
Effective length of query: 385
Effective length of database: 384
Effective search space:   147840
Effective search space used:   147840
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