GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Rhodobacter johrii JA192

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  302 bits (774), Expect = 2e-86
 Identities = 176/503 (34%), Positives = 296/503 (58%), Gaps = 15/503 (2%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ ++ ++  F  V+ L  VD  L PGEVHAL+GENGAGKST +K L G    +AG ++
Sbjct: 4   PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHE-KRGPFGIDWKKTHEAA 124
           +DG+P  F  + +A+ AG+  ++QE NL T L+V EN+ LG E KRGPF +D +     +
Sbjct: 64  LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPF-LDHRAMQAES 122

Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184
           ++ L ++   ++DP   +S++S+  +Q+V IA+A+ + A+VLI+DEPT+ L   E   L 
Sbjct: 123 RRLLERLHC-AVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181

Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244
             + ++R +G AIL+ SH LD++  I DR+T+LR+G+ +     K    D +   M+G+ 
Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGR- 240

Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
             ELS +   K+    +P  +P+++V GL   G +      + +GEV+GFAGL+GSGRTE
Sbjct: 241 --ELSGLFPPKS----SPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTE 294

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI-L 363
           L   + G  +P +G   + G  +  +    A    + Y TE+R+++G++    + +N+ L
Sbjct: 295 LMEGIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTL 353

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           +AL     +   I K   +  + + + + ++R  D      +LSGGNQQK+L+ + +   
Sbjct: 354 LALDRFGRVL--IDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483
           P ++I+DEPTRGID+G K +I   +  LA++G  V+ +SSEL EV+ L++ + V+     
Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471

Query: 484 IAEIENDDTVSQATIVETIANTN 506
             E+E  + +++  IV      N
Sbjct: 472 AGEVEG-EAITEENIVRLAMGLN 493


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: 602
Number of extensions: 30
Number of successful extensions: 8
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: 513
Length of database: 499
Length adjustment: 34
Effective length of query: 479
Effective length of database: 465
Effective search space:   222735
Effective search space used:   222735
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 24 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