GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Lentibacillus jeotgali Grbi

Align ABC transporter related (characterized, see rationale)
to candidate WP_040912583.1 ON01_RS16055 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_000224785.1:WP_040912583.1
          Length = 491

 Score =  352 bits (904), Expect = e-101
 Identities = 182/496 (36%), Positives = 311/496 (62%), Gaps = 9/496 (1%)

Query: 7   LKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGE 66
           ++ ISK + G + L+ V+  +  GEVHAL+GENGAGKSTL+K++TG   +D G +   G+
Sbjct: 1   MQGISKSFSGNQVLKSVNFSVDKGEVHALVGENGAGKSTLIKILTGIHKRDEGAVRINGK 60

Query: 67  PQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR--RLGLIHFKKMYADARAV 124
             HF+ P +A++ GI  ++QE+N++P+LTV +N+FLG      + G+++ K+M    +A 
Sbjct: 61  EVHFSHPKEAEQQGIMVIHQELNIIPHLTVTENMFLGKNIAYGKTGILNTKEMRKQCKAN 120

Query: 125 LTQFKLD-IDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           L +  +  ID      D S+  QQ+I IAR V+ +A+++V+DEPTA+L  +E+  LF ++
Sbjct: 121 LERLGVSTIDPDDIAGDLSVGKQQMIEIARAVSTNAELIVMDEPTAALTDREIDSLFEVI 180

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
             L+  GVA+++I+H ++++++I DRITVLR+G++IG     ++    +++ M+GR L E
Sbjct: 181 QSLRKNGVAVIYISHRMEEIFRICDRITVLRDGEYIGTKNVTDVDFDGIVKMMVGRELGE 240

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
           +       ER  T  + V+  ++ ++ KG    ++ +V +G+ +G+AGL+G+GRSE+   
Sbjct: 241 RF-----PERDYTGGD-VIFEVKSLARKGLFDDISFSVKEGEILGVAGLMGAGRSEIMET 294

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363
           +FG     +GSIHL G++L +  P DAI AGI    EDRK  G++   SI +NI L    
Sbjct: 295 IFGYTHKQNGSIHLNGKELPIKHPSDAIKAGIGFITEDRKSKGLLTDFSIGDNISLTNMK 354

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
            +     +S  ++  +    +D+L++    A +  + LSGGNQQKV++A+WL IEP LL+
Sbjct: 355 SVSSNGIISANKEHRLIAELMDRLKVKATGATQEAKALSGGNQQKVVIAKWLGIEPKLLI 414

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483
           LDEPTRG+D+GA  EI  ++  L   G+++++ SS+L E++  S++++V+ +        
Sbjct: 415 LDEPTRGVDVGAKKEIYNIMNELTKNGVAIIMVSSDLPEVLGVSDRIMVIYEGRIANIFD 474

Query: 484 GAELTSQHVMQAIAEG 499
             +   +++M A A G
Sbjct: 475 RDQADQENIMTAAAGG 490


Lambda     K      H
   0.319    0.136    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: 556
Number of extensions: 27
Number of successful extensions: 7
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: 499
Length of database: 491
Length adjustment: 34
Effective length of query: 465
Effective length of database: 457
Effective search space:   212505
Effective search space used:   212505
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