GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Phyllobacterium brassicacearum STM 196

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_106712778.1 CU102_RS19520 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_003010955.1:WP_106712778.1
          Length = 505

 Score =  321 bits (822), Expect = 4e-92
 Identities = 173/470 (36%), Positives = 275/470 (58%), Gaps = 3/470 (0%)

Query: 5   LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSIL 64
           +LL A  + K++ G  AL    L++R G +HAL G NGAGKST + +L G+ Q D G + 
Sbjct: 6   VLLAARGICKSFIGFRALDAVDLTIRRGEIHALLGENGAGKSTLIKVLTGVHQPDLGVME 65

Query: 65  LNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124
           L+G P+      +A   GI  + QE+  +P M+VA+N+++GR+P R G  +D + + +R 
Sbjct: 66  LDGQPIHVRDTLQAQQLGIGTVYQEVNLLPNMSVADNLFVGRQPMRFG-FIDRRRMEKRA 124

Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184
           RELL   +  +D +S + R SVA  QLV IA+A     +++I+DEPT+++  HE + LF 
Sbjct: 125 RELLSQYDLHIDVSSDLSRYSVAVQQLVAIARAVDMSGRILILDEPTASLDRHETEILFA 184

Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244
            +RRL  +G GIV+++H L ++ +I D  ++ R+G    S   + + +  LV  ++G+ L
Sbjct: 185 TLRRLKERGLGIVFITHFLDQVYEICDRVTVLRNGKVAGSELTSQLPKMQLVSLMLGRAL 244

Query: 245 TRIDHKVGRECAANTCLQVD--NLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302
             + H V R+       Q     + R+       L + +GE++G+ GL+GSGR+E    +
Sbjct: 245 AAVTHNVRRDRQEPETKQFSFKGMGRSRSVAPFDLDIGEGEVIGMAGLLGSGRTETARLL 304

Query: 303 YGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKR 362
           +G+  AD+G   + G P+ I  P+  +  G  L  EDRK  G++   S+  NI L+   +
Sbjct: 305 FGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLCPEDRKTDGIIGDLSVRENIVLALQAQ 364

Query: 363 LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLC 422
              +  +  R++  LA+  VK L I+TT +E P+  +SGGNQQKV+LA+ L+T P  L+ 
Sbjct: 365 RGWFKRLPRRQQVALADKFVKALDIRTTDIEKPIKFLSGGNQQKVILARWLATNPRFLIL 424

Query: 423 DEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFK 472
           DEPTRGID GA  EI  L++Q    G A +V+SSE  E++  S R+ V +
Sbjct: 425 DEPTRGIDVGAHAEIIALINQLCDDGMALLVISSEIEEIVAYSTRVVVLR 474



 Score = 67.8 bits (164), Expect = 9e-16
 Identities = 57/220 (25%), Positives = 96/220 (43%), Gaps = 27/220 (12%)

Query: 27  LSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGIAMI 86
           L +  G V  + G  G+G++    +L GI   D G   ++G PV+   P +A+A G  + 
Sbjct: 279 LDIGEGEVIGMAGLLGSGRTETARLLFGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLC 338

Query: 87  TQELEP---IPYMTVAENI---------WLGREPRRAGCIVDNK---ALNRRTRELLDSL 131
            ++ +    I  ++V ENI         W  R PRR    + +K   AL+ RT       
Sbjct: 339 PEDRKTDGIIGDLSVRENIVLALQAQRGWFKRLPRRQQVALADKFVKALDIRT------- 391

Query: 132 EFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTA 191
               D   P+  LS    Q V +A+  + + + +I+DEPT  I       +   I +L  
Sbjct: 392 ---TDIEKPIKFLSGGNQQKVILARWLATNPRFLILDEPTRGIDVGAHAEIIALINQLCD 448

Query: 192 QGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADID 231
            G  ++ +S  + E+   +    + RD   V+ G +A  D
Sbjct: 449 DGMALLVISSEIEEIVAYSTRVVVLRDR--VQRGELAGDD 486


Lambda     K      H
   0.319    0.135    0.381 

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: 544
Number of extensions: 20
Number of successful extensions: 6
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: 495
Length of database: 505
Length adjustment: 34
Effective length of query: 461
Effective length of database: 471
Effective search space:   217131
Effective search space used:   217131
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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