GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Dinoroseobacter shibae DFL-12

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  371 bits (953), Expect = e-107
 Identities = 205/504 (40%), Positives = 315/504 (62%), Gaps = 16/504 (3%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVY-PAGT 59
           ++   L + +ITKTFPGVKAL +V+L +  G++ AL+GENGAGKST++K+L+G+Y P G 
Sbjct: 16  VSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDG- 74

Query: 60  YEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEV-ASNGVISWQ 118
             G I  +G    F     + D G+  IHQE  L   LS+AENIFLG+    + G+I W+
Sbjct: 75  --GRILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWK 132

Query: 119 QTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178
           +T    R LL  +G +  P+  + D+G+  + LV IA+ALS   +++I+DEPTA+L+  +
Sbjct: 133 KTTENARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKE 192

Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238
            E L  L+   + QG   + I+HK +E+ ++AD  TV RDG  +   D    +++E  ++
Sbjct: 193 IEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIG--DGAIADVTEADLV 250

Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298
           + MVGRD+   +P R   +G+T+L V+ +   H    D     DI+ T+R+GE++G  GL
Sbjct: 251 KMMVGRDVSQIFPQRAPNVGDTVLTVQGYA--HPTEFD-----DISFTLREGEILGFYGL 303

Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358
           +GAGR+EF  S+FG +      G V I G   ++S+   A+D G+ YV EDR   G +L+
Sbjct: 304 VGAGRSEFMQSLFGIT--RPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILD 361

Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
             I  N TL +L  +S+   +   +E  +A ++  RL +R++ +     NLSGGNQQKVV
Sbjct: 362 LPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVV 421

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           ++KWL + P V+ILDEPT+G+D+G+K  ++  + +LAA G  V+M+SSE+PE+LG  DR+
Sbjct: 422 IAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRV 481

Query: 479 YVMNEGRIVAELPKGEASQESIMR 502
            VM EGRIVAEL   +   E+++R
Sbjct: 482 IVMREGRIVAELAGDDLQPETLVR 505



 Score = 65.5 bits (158), Expect = 4e-15
 Identities = 59/257 (22%), Positives = 115/257 (44%), Gaps = 14/257 (5%)

Query: 251 PPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSV 310
           P  D P+ +  L + +     +     + L D+++++  G+V  + G  GAG++     +
Sbjct: 10  PSEDPPVSQAALALAHIT---KTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKIL 66

Query: 311 FGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLND--NILHNTTLA 368
            G        G +L+DG+PV  ST + A D G+  +     H   VL D  ++  N  L 
Sbjct: 67  TGIYQPDG--GRILVDGQPVPFSTPQAAADHGVTAI-----HQETVLFDELSVAENIFLG 119

Query: 369 NLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPD 428
           + A      +ID  K  + A    T +         +  +L   N+  V +++ L     
Sbjct: 120 H-APRGAFGLIDWKKTTENARALLTSIGAELDPD-HKLKDLGIANKHLVAIARALSIEAR 177

Query: 429 VLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVA 488
           V+I+DEPT  +      E+Y ++  L A GK +L IS +  E+    D   V  +G+++ 
Sbjct: 178 VVIMDEPTAALSHKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIG 237

Query: 489 ELPKGEASQESIMRAIM 505
           +    + ++  +++ ++
Sbjct: 238 DGAIADVTEADLVKMMV 254


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: 599
Number of extensions: 28
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 510
Length adjustment: 35
Effective length of query: 477
Effective length of database: 475
Effective search space:   226575
Effective search space used:   226575
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