GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Acidovorax sp. GW101-3H11

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  440 bits (1131), Expect = e-128
 Identities = 228/486 (46%), Positives = 327/486 (67%), Gaps = 7/486 (1%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ + GI  +F G+  L  V L LYPGE+HALMG+NGAGKST+IK LTGV + + G + 
Sbjct: 17  PVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMR 76

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKR----GPFGIDWKKTH 121
           + G+    +  L AQ  GI+TVYQEVNLC NLSV EN+  G   R      F IDW   H
Sbjct: 77  LGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLH 136

Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181
           + A+  +A++GL+ ID    LS   +A+QQLVAIARA+ I ++VLILDEPTSSLD +EV+
Sbjct: 137 QRARDLVARIGLQ-IDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195

Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
            LF ++R++R  G++I+FV+HFL+Q+Y ++DR+T+LRNG ++ E + KD     LI  M+
Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255

Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301
           G+  A  S+  A      +      ++  +GLG+   + P+D+ I  GEVVG AGLLGSG
Sbjct: 256 GRDLAAASEQPAPAPA--VDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSG 313

Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQN 361
           RTEL RLL+G ++PD G   ++G+ V  ++P  A+++ +A   E R+ +GI+ +L+VR+N
Sbjct: 314 RTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVREN 373

Query: 362 ILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421
           I +ALQA  G+ K + + E   + ++Y+K L ++    D+P+  LSGGNQQK ++ RW+A
Sbjct: 374 IALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMA 433

Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDR 481
             P LLILDEPTRGID+ AK EI   +L LA  GM V+FISSE+ EVVR++  I VL+DR
Sbjct: 434 IEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDR 493

Query: 482 HKIAEI 487
            K+ E+
Sbjct: 494 RKVGEL 499



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 18/247 (7%)

Query: 262 PGEKPIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDS 317
           P   P++ + G+ K+      +  V +++Y GE+    G  G+G++ L ++L G  +   
Sbjct: 13  PAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASG 72

Query: 318 GTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIP 377
           G   L G+ V    P  A   ++  ST  + +  +  +L+V +NI        G+ +   
Sbjct: 73  GQMRLGGQAVWPDSPLAA--QRLGISTVYQ-EVNLCPNLSVAENIFAGRYPRCGIAQGFR 129

Query: 378 ------KKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDE 431
                  + A  +V +   +++V     D PV       QQ V I R L+    +LILDE
Sbjct: 130 IDWATLHQRARDLVARIGLQIDVTRLLSDYPV-----AVQQLVAIARALSIESRVLILDE 184

Query: 432 PTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDD 491
           PT  +D     ++ +V+  L S+G+ +VF++  L +V  +SD I VL++   + E    D
Sbjct: 185 PTSSLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKD 244

Query: 492 TVSQATI 498
              QA I
Sbjct: 245 LGPQALI 251


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: 637
Number of extensions: 25
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: 517
Length adjustment: 35
Effective length of query: 478
Effective length of database: 482
Effective search space:   230396
Effective search space used:   230396
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