GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22220 HSERO_RS22220 D-ribose
           transporter ATP-binding protein
          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 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