GapMind for catabolism of small carbon sources

 

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

Align BilEB aka OpuBB protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)
to candidate WP_022528965.1 L248_RS04780 ABC transporter permease/substrate-binding protein

Query= TCDB::Q93A34
         (504 letters)



>NCBI__GCF_000469325.1:WP_022528965.1
          Length = 507

 Score =  528 bits (1361), Expect = e-154
 Identities = 277/508 (54%), Positives = 367/508 (72%), Gaps = 13/508 (2%)

Query: 4   LIDTFTVRKDELFTALVQHIQISFVSLFIAVLIALPLGIYLTRHKRLAEPIIQVAAIFQT 63
           +I T   R+ +L +AL QH+ IS ++L IA++IA+PL  +  RH + A  ++Q+A I QT
Sbjct: 3   IISTLVDRRQQLLSALGQHLSISLIALVIAIIIAMPLAFWAARHSKAAAVLLQIAGILQT 62

Query: 64  IPSLALLGLLIPLVGIGIVPAIIALVIYALLPILRNTYTGIKEVDPALVEASRAMGMNKW 123
           IPSLALLGLLIPLVGIG  PA+IALVIYALLPI +NTY GI  +DPAL EA+ A GM +W
Sbjct: 63  IPSLALLGLLIPLVGIGTTPAVIALVIYALLPIFQNTYIGITGIDPALEEAADAFGMGRW 122

Query: 124 KRLYKVQLPLAMPVIMAGIRTAMVLIIGTATLAALIGAGGLGDLILLGIDRNDNSLILLG 183
           ++L KV+LPLA P I+ GIRTA+VLIIGTATLAALIGAGGLG  ILLGIDRN+ +LI++G
Sbjct: 123 RKLRKVELPLAAPTIIGGIRTALVLIIGTATLAALIGAGGLGSFILLGIDRNNTALIVIG 182

Query: 184 AIPAALLAILFDFLLRFLEKASFKSTIITISAGILLTAAIIV----VPYFASDKKEITVA 239
           A+ +ALLAI+   L+ +L K  ++ T     AG+++   + V    +    +  + + +A
Sbjct: 183 AVFSALLAIILSALISWLAKQRWQWT-----AGLVVLLILGVGGTQIASRVNQPETVVIA 237

Query: 240 GKLGAEPEILINMYKLVIE-DETDLKVNVKPNMGKTSFVFNALKSGDIDIYPEFTGTVLE 298
           GKLG+EP+ILINMYK +IE D+  ++V +K N GKT+F+FNA+K+G +DIYPEFTGTVLE
Sbjct: 238 GKLGSEPDILINMYKQLIEHDDPHIRVQLKSNFGKTTFLFNAVKTGSVDIYPEFTGTVLE 297

Query: 299 TFLKEN--AKTHDPEEVYTQARDGLAKDFDMTYLKPMKYNNTYALAVSPEFAKENNLEKI 356
           T +K++  A      + YT AR  L+K F MTYL+PM Y NTY +AV   FA+++ L  I
Sbjct: 298 TLVKQDRTAAHLTAAQTYTAARQALSKQFQMTYLQPMAYQNTYGVAVKRRFAQDHGLTTI 357

Query: 357 SDLGPVSDQVKAGFTLEFKDRSDGYKGIQDKYGLTFSNLKTMEPKLRYNAIKSGDINLLD 416
           S L  V+DQ+ AGFTLEF DR DGY+G++  YGL F    + EP LRY AI +G +NL+D
Sbjct: 358 SSLRNVTDQLSAGFTLEFLDRPDGYQGLKKVYGLHFPT-HSFEPALRYAAINNGKVNLVD 416

Query: 417 AYSTDSELAQYKLKVLEDDQQLFPPYQGAPLMLTKTLDKYPELKKPLNKLAGKITDDEMR 476
            YSTDSE+ QYKL+VL DD+ LFPPYQGAPLM T    ++P + + LNKLAG ITD +M+
Sbjct: 417 VYSTDSEIVQYKLQVLRDDKHLFPPYQGAPLMRTAFARQHPGIVRSLNKLAGHITDKQMQ 476

Query: 477 KMNYEVNVNGKSAYTVAKDYLKDQGIIK 504
           +MNY VNV  +S   VA+ YL   G++K
Sbjct: 477 QMNYAVNVRNESPAKVARTYLTSHGLLK 504


Lambda     K      H
   0.320    0.139    0.387 

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: 581
Number of extensions: 19
Number of successful extensions: 5
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: 504
Length of database: 507
Length adjustment: 34
Effective length of query: 470
Effective length of database: 473
Effective search space:   222310
Effective search space used:   222310
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