GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Phaeobacter inhibens BS107

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Phaeo:GFF385
          Length = 509

 Score =  272 bits (695), Expect = 2e-77
 Identities = 168/500 (33%), Positives = 272/500 (54%), Gaps = 24/500 (4%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P + +KGI+  F  V+A   + + + PG +H ++GENGAGKST++  L G YK + G + 
Sbjct: 4   PAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVW 63

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           + GK  +   +  A +AGI  V+Q   L  N +V EN++LG E  G       K  ++ K
Sbjct: 64  IHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKARKSLK 123

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
              A+  L ++DP   +  I + MQQ V I +A+   A +LILDEPT  L   E   LF 
Sbjct: 124 DLAAEYEL-NVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFR 182

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           I+ ++R  G  I+ ++H L +I E TD ++++R G+    V T +T  + L  +M+G+  
Sbjct: 183 ILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKV 242

Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKK-----GTINPVDVDIYKGEVVGFAGLLGS 300
             L ++    A    TPG KPI++++ L          +  +D+ +  GE++G AG+ G+
Sbjct: 243 --LLRVDKVPA----TPG-KPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGN 295

Query: 301 GRTELGRLLYGADKPDSGTYTLNGKKVNIS----DPYTALKNKIAYSTENRRDEGIIGDL 356
           G++EL  +L G  +   G+  LNG  + +S    D        +A+  E+R+ EG+I D 
Sbjct: 296 GQSELMEVL-GGMREGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDF 354

Query: 357 TVRQNILI----ALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQ 412
              +N+      A +  RG+        AD   +  M + +VRP DP    KN SGGNQQ
Sbjct: 355 HAWENVAFGYHHAPEYQRGLLMNNAALRADT--EAKMAKFDVRPPDPWLAAKNFSGGNQQ 412

Query: 413 KVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLS 472
           K+++ R +  +PELL++ +PTRG+DIGA   I + +++L  QG  ++ +S ELEE++ L+
Sbjct: 413 KIVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLA 472

Query: 473 DDIEVLKDRHKIAEIENDDT 492
           D + V+ D   + E   D T
Sbjct: 473 DRVAVMFDGMIMGERPADQT 492



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 65/253 (25%), Positives = 119/253 (47%), Gaps = 13/253 (5%)

Query: 2   TDKNPIVVMKGITI-EFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60
           T   PI+ ++ +++ +  GV  +  +DLT+  GE+  + G  G G+S +++ L G+ +  
Sbjct: 252 TPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLGGMRE-G 310

Query: 61  AGSIMVDGKPQQFNGT-LDAQNAGIATVY------QEVNLCTNLSVGENVMLGHEKRGPF 113
            GSI ++G P   +G   DA+    A V       Q   L  +    ENV  G+     +
Sbjct: 311 QGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGYHHAPEY 370

Query: 114 GIDWKKTHEAAKK----YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILD 169
                  + A +      +A+  +   DP     + S   QQ + +AR +  N ++L++ 
Sbjct: 371 QRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNPELLLIG 430

Query: 170 EPTSSLDANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTK 229
           +PT  +D   +  +   + ++RD G AIL VS  L++I  + DR+ ++ +G  + E    
Sbjct: 431 QPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIMGERPAD 490

Query: 230 DTPRDELIGMMIG 242
            T   EL  +M G
Sbjct: 491 QTDEKELGLLMAG 503


Lambda     K      H
   0.316    0.135    0.376 

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: 643
Number of extensions: 39
Number of successful extensions: 9
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: 513
Length of database: 509
Length adjustment: 35
Effective length of query: 478
Effective length of database: 474
Effective search space:   226572
Effective search space used:   226572
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