Alignments for a candidate for fruK in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Desulfovibrio vulgaris Hildenborough

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  246 bits (627), Expect = 2e-69
 Identities = 160/495 (32%), Positives = 261/495 (52%), Gaps = 22/495 (4%)

Query: 3   DKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62
           D  P+V ++GI   F  V+A   + L + PG + AL+GENGAGKST++  L+G    + G
Sbjct: 30  DVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTG 89

Query: 63  SIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTH- 121
            I VDG+  +F    DA  AGI  VYQ   L  +++V ENV+LG       G      H 
Sbjct: 90  IIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-----GAWLSPVHM 144

Query: 122 -EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEV 180
                +  A+ GL+ IDP   +  +S+  +Q V I + +  +++VLILDEPT+ L   E 
Sbjct: 145 SRVVAELAARYGLD-IDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGET 203

Query: 181 RDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRD-ELIGM 239
             LF  + ++ ++G AI+F+SH + ++  + D + ILR G+ + E    + P + EL   
Sbjct: 204 EQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANR 263

Query: 240 MIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLG 299
           M+G+      ++  + A   + PG++ ++ V GL   G +  +  ++ KGEV   AG+ G
Sbjct: 264 MVGR------EVILEVAAEPLEPGDR-VLHVDGLAGDG-LKGLSFEVRKGEVFAIAGVAG 315

Query: 300 SGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVR 359
           +G+ EL   + G  +P  G   L G            +  +AY  E+R+       L + 
Sbjct: 316 NGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLV 375

Query: 360 QNILIALQA--TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIG 417
            N L+  +   TRG F  + +K ADA     + E NV+P   + P ++LSGGN QK+++G
Sbjct: 376 DNFLLTARGCFTRGPF--LDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVG 433

Query: 418 RWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV 477
           R     P L++ + PT+G+DI A  E+   +L++ S   GV+ +S +L EV+ L+D + V
Sbjct: 434 REFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAV 492

Query: 478 LKDRHKIAEIENDDT 492
           +     I  ++  DT
Sbjct: 493 MYRGCFIGLLDRSDT 507



 Score = 85.9 bits (211), Expect = 3e-21
 Identities = 64/247 (25%), Positives = 119/247 (48%), Gaps = 15/247 (6%)

Query: 266 PIVDVKGLGKK-GTI---NPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321
           P+V ++G+GK  G +   + + +DI  G +    G  G+G++ L  +L G    D+G   
Sbjct: 33  PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92

Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEA 381
           ++G+ V    P  ALK  I    ++     ++  +TV +N+L+          P+     
Sbjct: 93  VDGEAVRFRSPKDALKAGIGMVYQHFM---LVDSMTVAENVLLGQSGA--WLSPVHMSRV 147

Query: 382 DA-IVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGA 440
            A +  +Y  ++     DP   V +LS G +Q+V I + L     +LILDEPT  +  G 
Sbjct: 148 VAELAARYGLDI-----DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGE 202

Query: 441 KAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVE 500
             ++ + +  +A  G  +VFIS +++EV+ L+D+I +L+    + E    +   +A +  
Sbjct: 203 TEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELAN 262

Query: 501 TIANTNV 507
            +    V
Sbjct: 263 RMVGREV 269



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 60/231 (25%), Positives = 114/231 (49%), Gaps = 8/231 (3%)

Query: 23  LDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNA 82
           L G+   +  GEV A+ G  G G+  +++ +TG+ +   G + + G P +   T   +  
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354

Query: 83  GIATVYQE---VNLCTNLSVGENVML---GHEKRGPFGIDWKKTHEAAKKYLAQMGLESI 136
           G+A + ++   +  C +L + +N +L   G   RGPF +D K    AA+  LA+  ++  
Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPF-LDRKSADAAARDILAEYNVQPG 413

Query: 137 DPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVA 196
               P  S+S    Q + + R       +++ + PT  LD     +++A + +VR S   
Sbjct: 414 RAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVR-SHAG 472

Query: 197 ILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAE 247
           +L VS  L+++  + DR+ ++  G FI  +   DT + + IG+M+   + E
Sbjct: 473 VLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVSCE 523


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: 632
Number of extensions: 37
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: 524
Length adjustment: 35
Effective length of query: 478
Effective length of database: 489
Effective search space:   233742
Effective search space used:   233742
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:

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
the source code
instructions for running GapMind on your computer

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