GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_607 Predicted
           L-arabinose ABC transport system, ATP-binding protein
          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 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