GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pbgal in Burkholderia phytofirmans PsJN

Align 6-phospho-beta-galactosidase; EC 3.2.1.85; Beta-D-phosphogalactoside galactohydrolase; PGALase; P-beta-Gal; PBG (uncharacterized)
to candidate BPHYT_RS29195 BPHYT_RS29195 beta-glucosidase

Query= curated2:Q97EZ2
         (474 letters)



>FitnessBrowser__BFirm:BPHYT_RS29195
          Length = 470

 Score =  286 bits (732), Expect = 1e-81
 Identities = 166/464 (35%), Positives = 248/464 (53%), Gaps = 35/464 (7%)

Query: 6   EDFIFGGATAAYQAEGATKEDGKGPCIWDEYLKKEGRF----TGDTASDFYHKYKEDLKF 61
           + F+ G ATA+YQ EGA  EDG+ P IWD +  K G+     TG  A D YH+++ D+  
Sbjct: 34  KSFLLGAATASYQIEGAVNEDGRLPSIWDTFSAKPGKVLAGDTGAVACDHYHRWQADVDL 93

Query: 62  SRKFGVNGIRISIAWSRVIPDGKGEVNPKGLKFYSDLIDECIKNNVEPFVTLHHFDTPLT 121
               G+   R+SIAW RV+ D  G  N KGL FY  L+    +  +  FVTL+H+D P  
Sbjct: 94  LAGLGLEAYRLSIAWPRVM-DAAGAPNRKGLDFYKRLLARLKEKGITTFVTLYHWDLPQH 152

Query: 122 LFKDGDWLNRNNIDYFVRFAKVCFEALGDRVKKWITFNEAWAVAQNGYIIGNFPPSIKYD 181
           L   G WLNR+    F  +A +    L   V  W+T NE W  A  GY  G+  P +  D
Sbjct: 153 LEDCGGWLNRDTAYRFADYADLMSRELAGSVDAWMTLNEPWCSAYLGYGNGHHAPGLA-D 211

Query: 182 IPKAAQSMHNMMVAHAKVVELYKSMNLDGEIGIVHTLEGKYPITDSKEDKEAAYLDYMIS 241
              A Q+MH++++AH   V + ++ +   ++GIV  +      ++S  D+ AA+L  +  
Sbjct: 212 ARYATQAMHHLLLAHGLAVPVLRANDPASQVGIVANIGRGTANSESAADQRAAHLFEVQH 271

Query: 242 NKFMLDACFKGEYPKETEKTINEIMSKNGGELKIYDGDLEVLKKASSKIDFLGMNYYSSH 301
           N ++LD   KG YP++    + E+    G E  + DGD++ +   ++ +DFLG+NYY   
Sbjct: 272 NAWILDPLLKGSYPQD----LFELWP--GTEPLVLDGDMQTI---AAPLDFLGINYYF-- 320

Query: 302 FLKAYEGESRIHHNGTGEKGTSIFALKGIGERVNNPEVPTTDWDWPIYPKGLHDMLVRIK 361
                    R +    G  G     L+G+ ER        T   W +YP GL D+L   K
Sbjct: 321 ---------RTNVASDGAHGFRDVPLEGV-ER--------TQMGWEVYPDGLRDLLTGFK 362

Query: 362 NEYPNYKKIYVTENGMGYKDDFKDGKIDDTPRIDYINKHLEAILKAKNEGVVVKGYFVWS 421
             Y N   IY+TENGM   D   DG+++D+ RI ++ +HL A+ +A   GV ++GYF+WS
Sbjct: 363 ATYANLPPIYITENGMASDDKVIDGQVEDSQRISFLKRHLSAVDQAIKAGVEIRGYFLWS 422

Query: 422 LMDVLSWSNGYNKRYGLFYVDFKTQNRYAKKSAYWFKRISYEKK 465
           LMD   W+ GY +R+G+ +VD+ TQ R  K+SA    +   E+K
Sbjct: 423 LMDNFEWAFGYERRFGIVHVDYATQKRTIKRSANLVSKFLKERK 466


Lambda     K      H
   0.318    0.138    0.427 

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: 651
Number of extensions: 36
Number of successful extensions: 6
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: 474
Length of database: 470
Length adjustment: 33
Effective length of query: 441
Effective length of database: 437
Effective search space:   192717
Effective search space used:   192717
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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