GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Acidovorax sp. GW101-3H11

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 496

 Score =  303 bits (775), Expect = 1e-86
 Identities = 175/475 (36%), Positives = 276/475 (58%), Gaps = 12/475 (2%)

Query: 8   VVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVD 67
           V  + +T EF  V+ L GV   L PG V+ L+GENGAGKST++K L G      G ++VD
Sbjct: 5   VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64

Query: 68  GKPQQFNGTLDAQNA-GIATVYQEVNLCTNLSVGENVMLGHE-KRGPFGIDWKKTHEAAK 125
           G  +   G   A  A GI  ++QE NL  +L++ +N+ LGHE KRG F +D K   E  +
Sbjct: 65  GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLF-LDDKAMREKTR 123

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
           + LA++GL  +DP T +  + +A +QLV IARA+  NA++LI+DEPT++L   E   LFA
Sbjct: 124 EALAKVGLP-LDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFA 182

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           +M  ++ +GV I+++SH LD++   TD + ++R+G  +    T    R ++  +M+G+  
Sbjct: 183 LMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGREL 242

Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305
           A+L        +        P + V+GL   G    VD ++ +GE++GFAGL+G+GRTEL
Sbjct: 243 ADLF-----PPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTEL 297

Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA 365
              L G     +GT  + G+ V +  P  A ++ + Y +E+R+ +G+     +R N  + 
Sbjct: 298 FEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPN--LT 355

Query: 366 LQATRGMFKP-IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424
           L A     KP +      A + + ++E  +R    +    +LSGGNQQK+ + + L   P
Sbjct: 356 LMALERYAKPWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGP 415

Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLK 479
            +++LDEPTRG+D+GAK EI  +V  LA QG+ V+ ISSEL E++ L   + V++
Sbjct: 416 SVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMR 470



 Score = 88.2 bits (217), Expect = 6e-22
 Identities = 57/244 (23%), Positives = 121/244 (49%), Gaps = 8/244 (3%)

Query: 3   DKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62
           D  P + ++G+T+  PG    +GVD  +  GE+    G  GAG++ + + L G+    AG
Sbjct: 255 DGAPAITVRGLTV--PGWA--EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAG 310

Query: 63  SIMVDGKPQQFNGTLDAQNAGIATVYQE---VNLCTNLSVGENV-MLGHEKRGPFGIDWK 118
           ++ + G+P Q     DA   G+  + ++     L  +  +  N+ ++  E+     +D  
Sbjct: 311 TVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALERYAKPWLDPA 370

Query: 119 KTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDAN 178
               A ++ + + G+ +       SS+S   QQ +A+A+ +     V++LDEPT  +D  
Sbjct: 371 AEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVG 430

Query: 179 EVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIG 238
             R+++ +++++ + G+A++ +S  L ++  +  R+ ++R G+    +       +ELI 
Sbjct: 431 AKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIA 490

Query: 239 MMIG 242
              G
Sbjct: 491 HATG 494



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 61/214 (28%), Positives = 105/214 (49%), Gaps = 13/214 (6%)

Query: 271 KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNIS 330
           K  G    ++ V   +  G V G  G  G+G++ L ++L G + P +G   ++G    + 
Sbjct: 12  KEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGA---VR 68

Query: 331 DPYTALKNKIAYSTENRRDE-GIIGDLTVRQNILIALQATRGMF---KPIPKKEADAIVD 386
            P    +   A        E  +  DLT+ QNI +  +  RG+F   K + +K  +A+  
Sbjct: 69  APGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTREALAK 128

Query: 387 KYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQ 446
             +      P DPD  V+ L    +Q V I R LA +  LLI+DEPT  +  G    +  
Sbjct: 129 VGL------PLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFA 182

Query: 447 VVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
           ++  L + G+ +++IS +L+EV R +D++ V++D
Sbjct: 183 LMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRD 216


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: 621
Number of extensions: 28
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 513
Length of database: 496
Length adjustment: 34
Effective length of query: 479
Effective length of database: 462
Effective search space:   221298
Effective search space used:   221298
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