GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Caulobacter crescentus NA1000

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  333 bits (854), Expect = 9e-96
 Identities = 190/503 (37%), Positives = 305/503 (60%), Gaps = 17/503 (3%)

Query: 13  ITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKP-Q 71
           ++  FPGV+ALD VDL +  GEVHAL+GENGAGKST+IK L+  +  +AG++   G+   
Sbjct: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68

Query: 72  QFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQM 131
             +  L  Q  GIAT+YQE NL   LSV EN+ LG E R    +DW +    A+  L  +
Sbjct: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128

Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191
           GL  ++P  P+  +++A QQ+V IA+AM +NA+++I+DEPT++L   EV  L AI+  ++
Sbjct: 129 GLP-LNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLK 187

Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQI 251
              V++++VSH L ++  + DR T++R+G+F+      D    +++ +M+G+      + 
Sbjct: 188 ARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV----EF 243

Query: 252 GAKKARREITPGEKPIVDVKG-------LGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
             +K RR   P    ++ V+G       L   G +  V      GE+VG AGL+G+GRT+
Sbjct: 244 ERRKRRR---PPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI-L 363
           L RL++GAD   +G   ++ K + +  P  A++  I    E+R+ +G   D ++R+N+ L
Sbjct: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
            +L+A   + + + ++    +V+ Y ++L ++ AD +  +  LSGGNQQKVL+GR +A  
Sbjct: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483
           P++LI+DEPTRGIDIGAKAE+ QV+ DLA  G+ VV ISSEL EV+ +SD I V ++   
Sbjct: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480

Query: 484 IAEIENDDTVSQATIVETIANTN 506
           +A+++      +  +      T+
Sbjct: 481 VADLDAQTATEEGLMAYMATGTD 503


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: 648
Number of extensions: 31
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 513
Length of database: 515
Length adjustment: 35
Effective length of query: 478
Effective length of database: 480
Effective search space:   229440
Effective search space used:   229440
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