GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Bradyrhizobium sp. BTAi1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  454 bits (1167), Expect = e-132
 Identities = 241/497 (48%), Positives = 339/497 (68%), Gaps = 5/497 (1%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           ++ ++G+T  F  +KAL  VD TL  GE+HAL+GENGAGKST+IK +TGV+  +AG++ +
Sbjct: 14  LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126
            G         DA  AGIATVYQEVNL  NLSV +N+ LG +      +   +    A  
Sbjct: 74  AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHA 133

Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186
            L   GL+ ID   PL+S S+A+Q + AIARA+ ++A+VLILDEPT+SLD +EV  LF +
Sbjct: 134 LLLDYGLD-IDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRV 192

Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246
           MRK+   G+ I+FVSHFLDQ+YEI DR+T+LRNG+ I      D PR +LI MM+G+  A
Sbjct: 193 MRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLDLIRMMLGRELA 252

Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELG 306
           E +    ++A  +     +  V  KG GK+G + P D+++ +GEVVG AGLLGSGRTE  
Sbjct: 253 ETTH---ERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETA 309

Query: 307 RLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIAL 366
           RL++GA++ DSG  ++ GK V ++ P  A      Y  E R+ EGI+ DLTVR+NI++AL
Sbjct: 310 RLVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLAL 369

Query: 367 QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426
           QA RG+ +P+ ++E D I  +Y++ L++RP DP+RP+  LSGGNQQK L+ RWLAT P+L
Sbjct: 370 QARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKL 429

Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486
           L+LDEPTRGID+GA AEI ++V DL  QG+ ++ ISSEL+E+V  S+ + VL+DR  + E
Sbjct: 430 LVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEE 489

Query: 487 IENDDTVSQATIVETIA 503
           ++  D V  ++I+  IA
Sbjct: 490 LKG-DAVEVSSILAAIA 505


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: 679
Number of extensions: 26
Number of successful extensions: 7
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: 516
Length adjustment: 35
Effective length of query: 478
Effective length of database: 481
Effective search space:   229918
Effective search space used:   229918
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 Apr 09 2024. 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