Alignments for a candidate for fruK in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Moritella dasanensis ArB 0140

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_017221119.1 A923_RS0107850 ribose ABC transporter ATP-binding protein RbsA

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_000276805.1:WP_017221119.1
          Length = 501

 Score =  339 bits (869), Expect = 2e-97
 Identities = 190/477 (39%), Positives = 295/477 (61%), Gaps = 14/477 (2%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           I+ + GI   FPGVKALD   L +YPG+V AL+GENGAGKST++K LTG+Y ++ GSI  
Sbjct: 5   ILKLSGIEKSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINY 64

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPF-GIDWKKTHEAAK 125
            G    F+G   +Q  GI+ ++QE+NL   L++ EN+ LG E    F GI W +    A 
Sbjct: 65  QGSDVTFDGPRHSQEVGISIIHQELNLIPELTIAENIYLGRETTNAFGGIKWTQMFADAD 124

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
             L ++ ++       L  +S+  QQ+V IA+A+   ++V+++DEPT +L  +E + LF 
Sbjct: 125 ALLQRLNVKH-SSRQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETKSLFK 183

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           ++ ++R+ G  I+++SH L +I+EI D +T+LR+G+FI E+   D   D LI  M+G+  
Sbjct: 184 VINELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIEKMVGRRL 243

Query: 246 AEL-SQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
            E+  +I AK             ++V+ +   G +  V   +  GE++G +GL+G+GRTE
Sbjct: 244 DEIYPRIDAKHGTL--------CLEVENIVAPG-VRDVSFTLDHGEILGISGLMGAGRTE 294

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI-L 363
           L + +YGA    SG   L+ K V+   P   L N IAY +E+R+ +G+I  L+V++N+ L
Sbjct: 295 LMKAIYGALPRQSGDVILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSL 354

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
            AL A     +    KEA A+ D +M++ NV+    D+ + NLSGGNQQKV I + L T 
Sbjct: 355 CALDALSKGLQLDHAKEATAVED-FMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTR 413

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
           P++LILDEPTRG+D+GAK EI Q++    ++GM ++ +SSE+ EV+ +SD I V+ +
Sbjct: 414 PKVLILDEPTRGVDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHE 470



 Score = 97.8 bits (242), Expect = 8e-25
 Identities = 65/235 (27%), Positives = 120/235 (51%), Gaps = 8/235 (3%)

Query: 18  PGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTL 77
           PGV+    V  TL  GE+  + G  GAG++ ++KA+ G     +G +++D K        
Sbjct: 267 PGVR---DVSFTLDHGEILGISGLMGAGRTELMKAIYGALPRQSGDVILDDKVVSPITPR 323

Query: 78  DAQNAGIATVYQEVN---LCTNLSVGENVMLGHEKRGPFGI--DWKKTHEAAKKYLAQMG 132
           D    GIA + ++     L   LSV EN+ L        G+  D  K   A + ++ Q  
Sbjct: 324 DGLANGIAYISEDRKGDGLILGLSVKENMSLCALDALSKGLQLDHAKEATAVEDFMRQFN 383

Query: 133 LESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRD 192
           +++      + ++S   QQ VAIA+ ++   KVLILDEPT  +D    ++++ ++ + + 
Sbjct: 384 VKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKA 443

Query: 193 SGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAE 247
            G++I+ VS  + ++  ++DR+ ++  G+   E M  D  +++L+   +GK   E
Sbjct: 444 EGMSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADANQEKLMACAVGKKINE 498



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 60/208 (28%), Positives = 108/208 (51%), Gaps = 5/208 (2%)

Query: 284 VDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYS 343
           +++Y G+V+   G  G+G++ L ++L G    D G+    G  V    P  + +  I+  
Sbjct: 26  LNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINYQGSDVTFDGPRHSQEVGISII 85

Query: 344 TENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPV 403
               ++  +I +LT+ +NI +  + T   F  I   +  A  D  ++ LNV+ +     +
Sbjct: 86  ---HQELNLIPELTIAENIYLGRETTNA-FGGIKWTQMFADADALLQRLNVKHSSRQL-L 140

Query: 404 KNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISS 463
             LS G QQ V I + L+   +++++DEPT  +       + +V+ +L ++G G+V+IS 
Sbjct: 141 GELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETKSLFKVINELRNEGCGIVYISH 200

Query: 464 ELEEVVRLSDDIEVLKDRHKIAEIENDD 491
            L+E+  + DDI VL+D   IAEI   D
Sbjct: 201 RLKEIFEICDDITVLRDGKFIAEIAVTD 228


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: 676
Number of extensions: 30
Number of successful extensions: 8
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: 501
Length adjustment: 34
Effective length of query: 479
Effective length of database: 467
Effective search space:   223693
Effective search space used:   223693
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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