GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araF in Burkholderia phytofirmans PsJN

Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate BPHYT_RS19715 BPHYT_RS19715 ATPase

Query= SwissProt::P02924
         (329 letters)



>FitnessBrowser__BFirm:BPHYT_RS19715
          Length = 334

 Score =  283 bits (725), Expect = 3e-81
 Identities = 149/324 (45%), Positives = 211/324 (65%), Gaps = 5/324 (1%)

Query: 7   ALAAIGLAA--VMSQSAMAEN-LKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAV 63
           A+AA  LAA   M  SA A+  LK+GFLVK PE+ WF  E K A   G+  GF V+ I  
Sbjct: 12  AMAAAALAAPFAMQLSAHADAPLKVGFLVKMPEQAWFINEQKAASALGQKDGFSVVNIGT 71

Query: 64  PDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPM 123
           PDGEK L AID+L A GAKGFVIC PD +LG AI A+A+ Y+MK + VDDQ V++ GKP+
Sbjct: 72  PDGEKVLAAIDNLGAQGAKGFVICAPDVRLGPAIQARAKRYNMKFVTVDDQLVDSTGKPL 131

Query: 124 DTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALK 183
             VP + M+A KIG + G  + +EM++RGW  +E   + IT  EL TA+ RT G+  +L 
Sbjct: 132 PNVPHLGMSAFKIGNQVGTAISEEMKRRGWKPEEVGALRITNYELPTAKLRTDGATQSLL 191

Query: 184 AAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQG 243
           A GF ++ I+  P K+ D  G F+A++ +L QHP +K W+I  +N+ +VLGGVRATE   
Sbjct: 192 AGGFKKENIFDAPQKTTDDEGGFNASSPVLAQHPNIKKWVIFALNEESVLGGVRATEQLH 251

Query: 244 FKAADIIGIGINGV-DAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPK 302
             AAD+IG+GING  +A +E  K + TGFYG++  S  +HG +S+E L  W+    +PP 
Sbjct: 252 IPAADVIGVGINGAGEAFAEFQKKEPTGFYGTIAVSSTMHGKESTENLVEWIKDGKQPPA 311

Query: 303 FTEVTDVVLITRDNFKEELEKKGL 326
            T+ T  +++ R N+++  ++ G+
Sbjct: 312 DTQTTGKLMV-RSNWQDVRKELGI 334


Lambda     K      H
   0.315    0.132    0.381 

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: 320
Number of extensions: 9
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: 329
Length of database: 334
Length adjustment: 28
Effective length of query: 301
Effective length of database: 306
Effective search space:    92106
Effective search space used:    92106
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: 49 (23.5 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