GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Cupriavidus basilensis 4G11

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__Cup4G11:RR42_RS32890
          Length = 322

 Score =  219 bits (558), Expect = 8e-62
 Identities = 130/323 (40%), Positives = 199/323 (61%), Gaps = 12/323 (3%)

Query: 26  ARLFNPA---ARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTY 82
           A LF P    AR       +L L+ L  + AS  F+ + N++++L+  ++  +LA   T 
Sbjct: 4   ATLFPPLSADARSFAYRLFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTL 63

Query: 83  VIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKV 142
           VI+T G+DLSVG  +   A +A  V+   G  + LG+ A +  GAL G  +G+++A L++
Sbjct: 64  VILTGGLDLSVGANVAMSACVAATVMKATGSTM-LGVGAGLGTGALIGLANGLLVAMLRI 122

Query: 143 PPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILF 202
           PPFIAT GM+ +L G++        I+      F AI    L G     +PIP  ++++F
Sbjct: 123 PPFIATYGMLWVLHGVTYWFMAGETIH-GFPPAFRAIGSGYLWG-----VPIPVYLMLVF 176

Query: 203 LVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIAS 262
           LVA   + +  KT +G+  +A+G+N  A RLSGV V    V VY  SGA+ GIA L+  +
Sbjct: 177 LVA--GTAMSQKTTYGQEIYAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLA 234

Query: 263 RLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQE 322
           RLNSA+  +G+   L AIAAV+IGGTSL GG G + GT++GA I+++++NG+ +++V+  
Sbjct: 235 RLNSAEGDIGEALTLPAIAAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSAN 294

Query: 323 WQTVVTGVIIILAVYLDILRRRR 345
           WQ +VTGVI++LAV+LD L R+R
Sbjct: 295 WQPLVTGVIVVLAVFLDTLSRKR 317


Lambda     K      H
   0.326    0.139    0.398 

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: 282
Number of extensions: 23
Number of successful extensions: 4
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: 347
Length of database: 322
Length adjustment: 28
Effective length of query: 319
Effective length of database: 294
Effective search space:    93786
Effective search space used:    93786
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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