GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Lactobacillus shenzhenensis LY-73

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_000469325.1:WP_022530418.1
          Length = 508

 Score =  275 bits (702), Expect = 4e-78
 Identities = 165/472 (34%), Positives = 255/472 (54%), Gaps = 10/472 (2%)

Query: 14  VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73
           V+    + K F    AL+DV + +  GE HAL+G NGAGKSTL+ ++TG+ +  +G V  
Sbjct: 13  VLSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTL 72

Query: 74  SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133
            G        ++A    ++ VYQ   +  +LSVAEN++I RQP+R G IDW  M  DA  
Sbjct: 73  HGQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQIDWHRMNADAVK 132

Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193
           LL+   I V         SV  +Q++ IARA+   A  +ILDEPT+ LD +E+ +LF  I
Sbjct: 133 LLESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFAII 192

Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253
             L+ + +  LF++H + +VY I   +TVLR+ R+I       LP   L+  M G++   
Sbjct: 193 RHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIGQK--- 249

Query: 254 AVADAAARGALPADTAVALELKELTGADYEGV----SFTVKRGEVVGLTGATSSGRTSVA 309
              DA  +   P+     +    +      G+    S  V+ GEV+GL G   SGRT VA
Sbjct: 250 -FVDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVA 308

Query: 310 EAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTI 369
           E + G+     G I V    +   +   +LA  +G   +DR   G+V   S+ EN  +++
Sbjct: 309 ELLFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSL 368

Query: 370 ARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNV 429
               G   I    K+    QK ID L I     E  +  LSGGNQQKV++AR LAT+P +
Sbjct: 369 QAKKGLRRIPL-KKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKL 427

Query: 430 LVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVM 480
           L+L +PT G+D+ +K  + +++ ++  +G A++ +S E +++ RTCDR++V+
Sbjct: 428 LILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVL 479



 Score = 83.6 bits (205), Expect = 2e-20
 Identities = 63/244 (25%), Positives = 119/244 (48%), Gaps = 9/244 (3%)

Query: 10  SSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG 69
           S+V  V   +++KR      ++D S+ V  GE   L G  G+G++ +  +L G+   D G
Sbjct: 265 STVRFVRMEDISKR----GLVHDFSMAVRAGEVLGLAGLLGSGRTEVAELLFGVTHFDDG 320

Query: 70  EVRFSGAAAPSIADRDAWRERVACVYQH---STIIRDLSVAENLFINRQPLRG-GVIDWQ 125
            +         +  R A  +++    +    S I+ DLS+ EN+ ++ Q  +G   I  +
Sbjct: 321 VIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQAKKGLRRIPLK 380

Query: 126 AMRRDARALLDHWKIDVRE-DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGD 184
             +  A+  +D   I     + + GDLS   +Q V +AR L+   + +ILDEPT  +D +
Sbjct: 381 KQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKLLILDEPTRGIDIN 440

Query: 185 EIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIE 244
             + +   I +L R+G+  +FIS   +E+   C  + VLRD   +     + + ++ +++
Sbjct: 441 TKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGELTDNQISQDNIMK 500

Query: 245 AMTG 248
            + G
Sbjct: 501 VIAG 504


Lambda     K      H
   0.318    0.134    0.377 

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: 535
Number of extensions: 28
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 508
Length adjustment: 34
Effective length of query: 476
Effective length of database: 474
Effective search space:   225624
Effective search space used:   225624
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 (21.7 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