Alignments for a candidate for fruK in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Collimonas arenae Ter10

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_061533691.1 CAter10_RS12710 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_001584165.1:WP_061533691.1
          Length = 516

 Score =  446 bits (1146), Expect = e-129
 Identities = 239/495 (48%), Positives = 330/495 (66%), Gaps = 8/495 (1%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P + + GI   F GVKAL  V L LYPGEVH LMG+NGAGKST+IK LTGV+    G+I 
Sbjct: 18  PTLELNGIYKAFGGVKALSDVSLRLYPGEVHTLMGQNGAGKSTLIKVLTGVHIPEHGTIR 77

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           ++G+  +   TL+AQ+ GI+TVYQEVNLC NLSV EN+ +G        IDWK     A+
Sbjct: 78  LNGREVRPTSTLEAQHLGISTVYQEVNLCPNLSVAENIFIGRYPTKFGAIDWKTMQRQAQ 137

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
           + L  + ++ ID   PLS   +A+QQ+VAI+RA+ ++AKVLILDEPTSSLD  EV+ LF+
Sbjct: 138 RLLGDLQID-IDVTAPLSRYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQLLFS 196

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           ++RK+R+ G+AILFV+HFL+Q Y+I+DR+T+LRNG    E    +  R EL+  M+G   
Sbjct: 197 VLRKLREQGMAILFVTHFLEQTYDISDRITVLRNGVLEGEYRVDELTRLELVNKMVGSQM 256

Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305
              S++ A  A   +    + ++  +GLG+KG + P+D+D+  GEV G  GLLGSGRTE 
Sbjct: 257 Q--SEVQAPDAATGLRDNAEIVLQARGLGRKGILAPLDLDLRAGEVYGLCGLLGSGRTET 314

Query: 306 GRLLYGADKPDSGTYTLNGKKVN-ISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364
            RLL+GADK DSG  ++  K +     P  A+   I + +E+R+ EG I +L+VR+NI++
Sbjct: 315 ARLLFGADKADSGAISIKDKPLGKFGSPREAIAAGIGFCSEDRKQEGAILELSVRENIIL 374

Query: 365 ALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424
            LQA  G+ + IP+K   AI   Y+K L ++  D + P+ +LSGGNQQK L+ RWLAT P
Sbjct: 375 GLQARAGLLRVIPRKRQQAIAADYVKWLGIKTPDIETPISSLSGGNQQKALLARWLATDP 434

Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKI 484
            +LILDEPTRGID+ AK EI   V+ L  +GM ++FISSE+ EV+R SD + VL+DR   
Sbjct: 435 VILILDEPTRGIDVRAKQEIMDHVIALCRKGMAILFISSEISEVLRCSDRMLVLRDREPC 494

Query: 485 AEI----ENDDTVSQ 495
            E      +DD+V Q
Sbjct: 495 GEYLRGELDDDSVLQ 509



 Score = 99.4 bits (246), Expect = 3e-25
 Identities = 66/224 (29%), Positives = 118/224 (52%), Gaps = 6/224 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ-QFNGTLDAQNAGI 84
           +DL L  GEV+ L G  G+G++   + L G  K ++G+I +  KP  +F    +A  AGI
Sbjct: 291 LDLDLRAGEVYGLCGLLGSGRTETARLLFGADKADSGAISIKDKPLGKFGSPREAIAAGI 350

Query: 85  ATVYQE---VNLCTNLSVGENVMLGHEKRGPF--GIDWKKTHEAAKKYLAQMGLESIDPH 139
               ++         LSV EN++LG + R      I  K+    A  Y+  +G+++ D  
Sbjct: 351 GFCSEDRKQEGAILELSVRENIILGLQARAGLLRVIPRKRQQAIAADYVKWLGIKTPDIE 410

Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199
           TP+SS+S   QQ   +AR +  +  +LILDEPT  +D    +++   +  +   G+AILF
Sbjct: 411 TPISSLSGGNQQKALLARWLATDPVILILDEPTRGIDVRAKQEIMDHVIALCRKGMAILF 470

Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243
           +S  + ++   +DR+ +LR+ +   E +  +   D ++ ++ G+
Sbjct: 471 ISSEISEVLRCSDRMLVLRDREPCGEYLRGELDDDSVLQVIAGE 514


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: 684
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: 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 Sep 24 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 2024 update 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