GapMind for catabolism of small carbon sources

 

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

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  407 bits (1047), Expect = e-118
 Identities = 222/498 (44%), Positives = 324/498 (65%), Gaps = 14/498 (2%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           IL+++ ++K FPGV AL+ ++L ++ GE+HA+ GENGAGKSTLMK++SG Y A   +G I
Sbjct: 22  ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHAD--DGVI 79

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
            YEG    F + +D++  GI IIHQEL LVP LS+AENI+L  E      + ++      
Sbjct: 80  CYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNANA 139

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           +  L+++GL  SP TL+  + + +QQ+VEIAKALS   ++LI+DEPT+SL ES++  L  
Sbjct: 140 QRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFR 199

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           ++ E R  G+  + I+H+L+E+ ++ D++TVLRDG  + T D     I+E  I+  MVGR
Sbjct: 200 IIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINE--IVARMVGR 257

Query: 245 DLEDRYPPRD-VPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
            L+D YPPR+ VP  + ++ V++      Q  D      ++  +RKGE++G AGLMGAGR
Sbjct: 258 ALDDAYPPRESVPTEQVLMRVRDL-----QRTD--TFGPLSFDLRKGEILGFAGLMGAGR 310

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           TE A ++FG       +G + +   PV + + R+AI  G+AY++EDRK  GL L+  +  
Sbjct: 311 TEVARAIFGAE--RLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAA 368

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           N TL+N+  +S    +   +E  +A  +   L IR+  + Q   NLSGGNQQK+V+SKWL
Sbjct: 369 NITLSNVRAISSRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWL 428

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
           +    +L  DEPTRGIDVGAKY IY ++++LAADG GV++ISSE+PELLG  DRI V +E
Sbjct: 429 YRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHE 488

Query: 484 GRIVAELPKGEASQESIM 501
           G I A L   + SQE I+
Sbjct: 489 GLITAVLETRQTSQEEIL 506


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: 627
Number of extensions: 33
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: 515
Length adjustment: 35
Effective length of query: 477
Effective length of database: 480
Effective search space:   228960
Effective search space used:   228960
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