GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Lactobacillus shenzhenensis LY-73

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>NCBI__GCF_000469325.1:WP_022530418.1
          Length = 508

 Score =  282 bits (722), Expect = 2e-80
 Identities = 166/502 (33%), Positives = 279/502 (55%), Gaps = 20/502 (3%)

Query: 21  VHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHA 80
           + K F GV AL  V L  + G+++ L+GENG GKSTLIK+++G      G + + G    
Sbjct: 19  IAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTLHGQDIN 78

Query: 81  RLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTF---DRRVLAATA 137
             +  EA   GI TVYQ+++L PN+SVAENV +        GR    F   D   + A A
Sbjct: 79  PKTPQEAQDLGISTVYQEVNLCPNLSVAENVYI--------GRQPMRFGQIDWHRMNADA 130

Query: 138 ARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDN 197
            + LE++ +  + +   TL +   ++ +Q++AIARA+   A  +I+DEPT+SL   EV  
Sbjct: 131 VKLLESLDI--HVDVTKTL-DSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQ 187

Query: 198 LIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
           L A++ +LR Q + +LFV+H +D+ YAI   + VLR+G+ + +    +  +  +   M G
Sbjct: 188 LFAIIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIG 247

Query: 258 RHLSNERYRESAHAQDI----VLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNEL 313
           +   +   +    ++D      + +   ++ G   D S  +  GE+LG+ GLL SGR E+
Sbjct: 248 QKFVDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEV 307

Query: 314 ARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA 373
           A  L GV     G + +   ++    P  A   ++GY  EDR   G+  D  IR+N++ +
Sbjct: 308 AELLFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLS 367

Query: 374 MISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDP 433
           +    +    +I   + Q +A++ +  L I TP ++K +  LSGGNQQ+VL+ RWLA DP
Sbjct: 368 L--QAKKGLRRIPLKKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDP 425

Query: 434 RVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493
           ++LIL  PT G+D+ +K  I  ++ +LS++G+ II IS +  E+++ CDRI++++  H  
Sbjct: 426 KLLILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAV 485

Query: 494 AEYRADELSEADLYHALLSEAA 515
            E   +++S+ ++   +    A
Sbjct: 486 GELTDNQISQDNIMKVIAGGVA 507


Lambda     K      H
   0.319    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: 558
Number of extensions: 31
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 508
Length adjustment: 35
Effective length of query: 480
Effective length of database: 473
Effective search space:   227040
Effective search space used:   227040
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 (21.7 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