GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Lactobacillus shenzhenensis LY-73

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_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_000469325.1:WP_022530418.1
          Length = 508

 Score =  316 bits (809), Expect = 1e-90
 Identities = 178/492 (36%), Positives = 290/492 (58%), Gaps = 5/492 (1%)

Query: 5   LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSIL 64
           ++L   H+AK + GV AL D +L LRAG VHAL G NGAGKST + ++ G+ +R +G++ 
Sbjct: 12  VVLSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVT 71

Query: 65  LNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124
           L+G  +    P EA   GI+ + QE+   P ++VAEN+++GR+P R G I D   +N   
Sbjct: 72  LHGQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQI-DWHRMNADA 130

Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184
            +LL+SL+  VD T  +   SV+  Q++ IA+A      V+I+DEPTS++  +E   LF 
Sbjct: 131 VKLLESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFA 190

Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244
            IR L  Q   I++V+H + ++  I+D  ++ R+G ++      D+    LV  ++GQ+ 
Sbjct: 191 IIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIGQKF 250

Query: 245 TRID---HKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNC 301
              +   H+  ++ +    ++++++S+ G  HD S+ +R GE+LG+ GL+GSGR+E    
Sbjct: 251 VDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVAEL 310

Query: 302 IYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK 361
           ++G+T  D G + +    +    P+  +   +   +EDRK SG+V   SI  NI LS   
Sbjct: 311 LFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQA 370

Query: 362 RLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLL 421
           +      I  +K+ ++A+  +  L IKT S+E  +  +SGGNQQKV+LA+ L+T+P  L+
Sbjct: 371 K-KGLRRIPLKKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKLLI 429

Query: 422 CDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIST 481
            DEPTRGID   K+EI +L+ +  R G A I +SSE  E++   DRI V +    V   T
Sbjct: 430 LDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGELT 489

Query: 482 DTALSQEALLRL 493
           D  +SQ+ ++++
Sbjct: 490 DNQISQDNIMKV 501



 Score = 74.3 bits (181), Expect = 9e-18
 Identities = 54/224 (24%), Positives = 108/224 (48%), Gaps = 4/224 (1%)

Query: 22  LRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAA 81
           + D  +++RAG V  L G  G+G++    +L G+T  D G I +    V+   P +ALA 
Sbjct: 281 VHDFSMAVRAGEVLGLAGLLGSGRTEVAELLFGVTHFDDGVIYVGNDEVKRMNPRKALAD 340

Query: 82  GIAMITQELEP---IPYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDVDAT 138
            +   +++ +    +  +++ ENI L  + ++    +  K      ++ +D L+    + 
Sbjct: 341 QLGYCSEDRKVSGIVGDLSIRENIMLSLQAKKGLRRIPLKKQQEVAQKYIDLLDIKTPSM 400

Query: 139 SP-MHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIV 197
              +  LS    Q V +A+  + D +++I+DEPT  I  +  + +   I +L+ QG  I+
Sbjct: 401 EKKIGDLSGGNQQKVLLARWLATDPKLLILDEPTRGIDINTKREIENLIVKLSRQGMAII 460

Query: 198 YVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241
           ++S    E+ +  D   + RD   V       I +D++++ I G
Sbjct: 461 FISSEYEEMVRTCDRIIVLRDRHAVGELTDNQISQDNIMKVIAG 504


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: 493
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: 495
Length of database: 508
Length adjustment: 34
Effective length of query: 461
Effective length of database: 474
Effective search space:   218514
Effective search space used:   218514
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.

Links

Downloads

Related tools

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