GapMind for catabolism of small carbon sources

 

Aligments 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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