Alignments for a candidate for fruK in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Echinicola vietnamensis KMM 6221, DSM 17526

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  337 bits (864), Expect = 6e-97
 Identities = 188/497 (37%), Positives = 294/497 (59%), Gaps = 6/497 (1%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           ++ +K IT EF GVKALD V L L  G V A++GENGAGKST++K L+GVY    G+I  
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI-DWKKTHEAAK 125
           +G P +F  T DAQ  GI  ++QE+NL   LS+ EN+ LG E   P G+ D  K H+ A 
Sbjct: 61  NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
           + L ++ L ++DP TP+S + +  QQLV IA+A+ + ++V+I+DEPTS++   EV  LF 
Sbjct: 121 QLLHRLKL-NVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           I+R +R  G AI ++SH LD+++ I DR  +LR+G+ I+    +    + LI  M+G+  
Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239

Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305
                   ++    +   +   V    +  K  +  ++ ++ KGEV+G  GL+G+GRTEL
Sbjct: 240 VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTEL 299

Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGII--GDLTVRQNIL 363
              L+G         TL GK      P  A+   +A   E+R+ +G++   DL    ++ 
Sbjct: 300 MEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLT 359

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           +      G    +  K+   +  KYM EL ++ +   + V+ LSGGNQQKV++ +WLAT 
Sbjct: 360 VVDSILSGGL--LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATR 417

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483
           P++L+LDEPTRGIDI AK EI +++  LA++G+G++ +SSEL E++ +SD + V+ +   
Sbjct: 418 PKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRL 477

Query: 484 IAEIENDDTVSQATIVE 500
            A I  D   S+  I++
Sbjct: 478 TANIPIDAQTSEDEILQ 494



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 63/239 (26%), Positives = 110/239 (46%), Gaps = 13/239 (5%)

Query: 265 KPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNG 324
           K  V VK L      + V +++  G V    G  G+G++ L ++L G      GT   NG
Sbjct: 9   KEFVGVKAL------DDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNG 62

Query: 325 KKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGM-FKPIPKKEADA 383
             V   +   A +  I       ++  +I  L++R+NI +  +    M    + K   +A
Sbjct: 63  DPVKFQNTRDAQEKGINII---HQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEA 119

Query: 384 IVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAE 443
               +  +LNV   DP+ PV  L  G QQ V I + L+   +++I+DEPT  I       
Sbjct: 120 AQLLHRLKLNV---DPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEI 176

Query: 444 IQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETI 502
           +  ++  L ++G  + +IS +L+E+  ++D   VL+D   I   E +    +A I + +
Sbjct: 177 LFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235


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: 639
Number of extensions: 28
Number of successful extensions: 8
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: 502
Length adjustment: 34
Effective length of query: 479
Effective length of database: 468
Effective search space:   224172
Effective search space used:   224172
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources