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_RS32895 RR42_RS32895 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__Cup4G11:RR42_RS32895
          Length = 318

 Score =  188 bits (478), Expect = 1e-52
 Identities = 102/297 (34%), Positives = 173/297 (58%), Gaps = 9/297 (3%)

Query: 43  LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102
           LLL+ L FS   P F+ V+NL++I   + +  ++A+  T +I+T G+DLS+G ++T C V
Sbjct: 25  LLLLSLGFSVTGPGFLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAVLTLCGV 84

Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162
           +  +V+      LPL + AA+  G   G ++G +++ L++PPF+ATLG + + +GL+LV 
Sbjct: 85  VLAMVMVATES-LPLALGAALLTGLAFGLLNGALVSWLEIPPFVATLGTLGVAQGLALVA 143

Query: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTF 222
           +  + +     E    I    L+G     +P+P  +  +F        +L  T FG Y F
Sbjct: 144 TDGQSVT-GIGEAIPLIYAGQLLG-----VPLPIWIAAVFYGLF--HWLLYHTRFGAYVF 195

Query: 223 ALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAA 282
           ALG N EAL+ SGV+++ + +AVY   G + G+A L++ +R+N+  P    G E DAIAA
Sbjct: 196 ALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIGLEFDAIAA 255

Query: 283 VVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLD 339
           V +GGT+   G G + GT++G   + VL NGL ++ V    Q    G+++++ + ++
Sbjct: 256 VAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLVLVVLLIE 312


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: 267
Number of extensions: 21
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: 318
Length adjustment: 28
Effective length of query: 319
Effective length of database: 290
Effective search space:    92510
Effective search space used:    92510
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