GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Burkholderia phytofirmans PsJN

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__BFirm:BPHYT_RS28215
          Length = 509

 Score =  361 bits (927), Expect = e-104
 Identities = 207/501 (41%), Positives = 307/501 (61%), Gaps = 14/501 (2%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           LE+R+ +K+F  V+AL + +L +  GE+HAL+GENGAGKST++K+L+GV+   T  GE+ 
Sbjct: 11  LELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDT--GELV 68

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNRT 124
            +G  R F    ++ D G+ +I+QE  L   LSIAENIF+G +     G I +       
Sbjct: 69  VDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREV 128

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
             LL  +G+    + L+  + +  QQ++EIAKALS +  +LI+DEPTA+L+  + E L  
Sbjct: 129 DGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFT 188

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           ++ + R + +  + ITH+L+EV  +  ++T++RDG   K  D    +++ + I+  MVGR
Sbjct: 189 IVRKLRERDVAILFITHRLDEVFALTQRVTIMRDG--AKVFDGLTTDLNTEAIVAKMVGR 246

Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304
           DLE  YP  + P GE  L V+             V  DI+  VR GE+V +AGL+GAGR+
Sbjct: 247 DLETFYPKAERPPGEVRLSVRGLTRVG-------VFKDISFDVRAGEIVALAGLVGAGRS 299

Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364
           E A ++FG       +G++ I GK +       A+ AGLA V EDR+  GL L  +I  N
Sbjct: 300 EVARAIFG--IDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARN 357

Query: 365 TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424
            ++  L  + K  +I    E ++A+ + TRLR+++         LSGGNQQKVVL KWL 
Sbjct: 358 ASMTVLGRLVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLA 417

Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484
           + P VLI+DEPTRGIDVGAK E+Y+ + +L  DG  VLMISSE+PE+LG  DR+ VM+EG
Sbjct: 418 TGPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEG 477

Query: 485 RIVAELPKGEASQESIMRAIM 505
           RI A++ + +A +E IM A +
Sbjct: 478 RISADIARADADEERIMGAAL 498


Lambda     K      H
   0.316    0.135    0.374 

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: 620
Number of extensions: 37
Number of successful extensions: 10
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: 512
Length of database: 509
Length adjustment: 35
Effective length of query: 477
Effective length of database: 474
Effective search space:   226098
Effective search space used:   226098
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: 52 (24.6 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