GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Lactobacillus shenzhenensis LY-73

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000469325.1:WP_022530418.1
          Length = 508

 Score =  363 bits (933), Expect = e-105
 Identities = 197/494 (39%), Positives = 312/494 (63%), Gaps = 10/494 (2%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           V+++R++ K FPGV ALD+ Q +L AGEVHALMGENGAGKSTL+K+++GVY+R SG + L
Sbjct: 13  VLSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTL 72

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            G+ +    P++AQ LGI  ++QE+NL  +LS A+N++IGR+P +     ID   +N  A
Sbjct: 73  HGQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQ--IDWHRMNADA 130

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
             +   + + +D +  +   +V+ QQM+ IA+A+   + VLI+DEPT++L++ E+A+LF 
Sbjct: 131 VKLLESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFA 190

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG-RA 260
           IIR L+ Q + I++++H MD++  I+DR++V+R+G+YI     ++     +++ M+G + 
Sbjct: 191 IIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIGQKF 250

Query: 261 LDGEQRIPPDTSRNDVVLEVR--GLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARA 318
           +D   +    +     V  VR   +++   + D S  +R GE+LG AGL+G+GRTEVA  
Sbjct: 251 VDANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVAEL 310

Query: 319 IFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMG 378
           +FG    + G I +   +    +P  A+A  +GY SEDRK  G+   + ++ NI LS   
Sbjct: 311 LFGVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQA 370

Query: 379 R--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436
           +    R+    Q   +E AQ Y+  L IKTPS+E++   LSGGNQQK+++A+WL  D  +
Sbjct: 371 KKGLRRIPLKKQ---QEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKL 427

Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496
           L  DEPTRGID+  K EI  L+  L+ QG AI+ ISSE  E++R   R++V+ +    GE
Sbjct: 428 LILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGE 487

Query: 497 LARADATQEKIMQL 510
           L     +Q+ IM++
Sbjct: 488 LTDNQISQDNIMKV 501



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 68/250 (27%), Positives = 127/250 (50%), Gaps = 19/250 (7%)

Query: 18  SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77
           S+V  + + ++ KR      + +    + AGEV  L G  G+G++ + ++L GV   D G
Sbjct: 265 STVRFVRMEDISKRG----LVHDFSMAVRAGEVLGLAGLLGSGRTEVAELLFGVTHFDDG 320

Query: 78  DILLDGKPVEITEPRQAQALGIGIIHQELN---LMNHLSAAQNIFIGREPRKAMGLFIDE 134
            I +    V+   PR+A A  +G   ++     ++  LS  +NI +  + +K +      
Sbjct: 321 VIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQAKKGLRRI--- 377

Query: 135 DELNRQAAAIFARMRLDM-DPSTP-----VGELTVARQQMVEIAKALSFDSRVLIMDEPT 188
             L +Q     A+  +D+ D  TP     +G+L+   QQ V +A+ L+ D ++LI+DEPT
Sbjct: 378 -PLKKQQEV--AQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLATDPKLLILDEPT 434

Query: 189 AALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETS 248
             ++     E+  +I  L  QG+ I++IS + +E+ +  DR+ V+RD   +  +   + S
Sbjct: 435 RGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGELTDNQIS 494

Query: 249 MDTIISMMVG 258
            D I+ ++ G
Sbjct: 495 QDNIMKVIAG 504


Lambda     K      H
   0.320    0.135    0.372 

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: 615
Number of extensions: 31
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: 520
Length of database: 508
Length adjustment: 35
Effective length of query: 485
Effective length of database: 473
Effective search space:   229405
Effective search space used:   229405
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