GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Herbaspirillum seropedicae SmR1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__HerbieS:HSERO_RS22220
          Length = 505

 Score =  326 bits (835), Expect = 1e-93
 Identities = 171/475 (36%), Positives = 286/475 (60%), Gaps = 7/475 (1%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ + GI   F GV AL  V  T+ PGEV AL+GENGAGKST++K LTG+++ + GSI 
Sbjct: 11  PVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIH 70

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKR--GPFGIDWKKTHEA 123
           + G+  +F    DA   GI  V+QE  +   LSV EN+ +G +     P  IDW++  + 
Sbjct: 71  LGGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRMEDE 130

Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183
           A+   A++ ++ +     +  +S+A +  V IARA+   A+V+I+DEPT++L  +E+ +L
Sbjct: 131 ARALFARLEVD-LPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGEL 189

Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243
           + I+ ++R +G A++F+SH  D+IY + DR T+LR+G+FI      D    +L+ +M+G+
Sbjct: 190 YRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGR 249

Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
              ++    A     +  P    +++VK L      + V   +  GE++GF GL+G+GR+
Sbjct: 250 EVGQVFSRAASNTEDQTAP----VLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRS 305

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
           E+   L+G      G   ++G++V +  P  A+ + +AY  E+R+ +G +  L + QNI 
Sbjct: 306 EVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNIT 365

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           + +    G F    ++    I  +  ++L ++ +   + V  LSGGNQQKV++ +WLAT 
Sbjct: 366 LPVLPGIGFFLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQ 425

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
           P +LILDEPT+GIDIG+KA + + + +L +QG+ V+ +SSEL EV+ +SD I V+
Sbjct: 426 PRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVM 480



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 69/241 (28%), Positives = 120/241 (49%), Gaps = 16/241 (6%)

Query: 266 PIVDVKGLGKK--GTINPVDVD--IYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321
           P++ + G+GK+  G +   DV   +  GEV+   G  G+G++ L ++L G  +PD G+  
Sbjct: 11  PVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIH 70

Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIP---- 377
           L G++V  +    A++  I   T   ++  +  +L+V +NI I  Q   G  + I     
Sbjct: 71  LGGREVRFASAQDAMRGGI---TAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRM 127

Query: 378 KKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGID 437
           + EA A+  +   +L VR       VK+LS   +  V I R L+   +++I+DEPT  + 
Sbjct: 128 EDEARALFARLEVDLPVRAR-----VKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALS 182

Query: 438 IGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQAT 497
                E+ +++  L   G  V+FIS + +E+  ++D   VL+D   IA  E  D   Q  
Sbjct: 183 HHEIGELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQL 242

Query: 498 I 498
           +
Sbjct: 243 V 243



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 53/211 (25%), Positives = 104/211 (49%), Gaps = 6/211 (2%)

Query: 24  DGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAG 83
           D V   + PGE+    G  GAG+S ++ AL G+     G++ +DG+  +      A   G
Sbjct: 282 DDVSFAVRPGEILGFYGLVGAGRSEVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHG 341

Query: 84  IATV---YQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA--AKKYLAQMGLESIDP 138
           +A V    Q      +L + +N+ L       F +   +  E   A++   Q+ L++   
Sbjct: 342 LAYVPEDRQRQGALLSLPIFQNITLPVLPGIGFFLRRHRRREIDIARRLCEQLELKASHF 401

Query: 139 HTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAIL 198
           H  ++ +S   QQ V +A+ +    +VLILDEPT  +D      +   + ++   G+A++
Sbjct: 402 HQHVAQLSGGNQQKVVLAKWLATQPRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVI 461

Query: 199 FVSHFLDQIYEITDRLTILRNGQFIKEVMTK 229
            VS  L ++  ++DR+ ++  G+ +++V ++
Sbjct: 462 LVSSELPEVMGMSDRIVVMHQGR-VQQVFSR 491


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: 593
Number of extensions: 22
Number of successful extensions: 7
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: 505
Length adjustment: 34
Effective length of query: 479
Effective length of database: 471
Effective search space:   225609
Effective search space used:   225609
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:

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