GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Burkholderia phytofirmans PsJN

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__BFirm:BPHYT_RS20745
          Length = 341

 Score =  487 bits (1253), Expect = e-142
 Identities = 247/339 (72%), Positives = 291/339 (85%)

Query: 7   SATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSI 66
           ++ S ++ + N  +  GLRAR+F P A QKLLAF SL+L+++FFSFASP FM++DN++ I
Sbjct: 2   TSQSDTSALGNKKTFSGLRARVFTPTALQKLLAFGSLILLLVFFSFASPAFMQMDNMLGI 61

Query: 67  LQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFG 126
           LQ+TAVNGVLAIACT+VIIT GIDLSVGT+MTF AV+ GV LT W +P+  G+ AAI  G
Sbjct: 62  LQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAVICGVFLTYWHLPMWTGVLAAIGTG 121

Query: 127 ALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIG 186
           A+ G +SG + AK+K+PPFIATLGMMMLLKGLSLV+S  +PIYF DTE F  I+QDSLIG
Sbjct: 122 AICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMISQDSLIG 181

Query: 187 DLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVY 246
           DL+PSLP+PNAVLILF +A+ +SI LN+T  GRYTFALGSNEEA+RLSGV VD WK+A+Y
Sbjct: 182 DLLPSLPVPNAVLILFFLAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIY 241

Query: 247 TFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFI 306
             SGAICGIAGL+IASRLNSAQPALGQGYEL+AIAAVVIGGTSLSGG GTILGTIIGAFI
Sbjct: 242 GLSGAICGIAGLLIASRLNSAQPALGQGYELEAIAAVVIGGTSLSGGAGTILGTIIGAFI 301

Query: 307 MSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345
           MSVL NGLRIMSVAQEWQ VVTG+IIILAVY DILRR++
Sbjct: 302 MSVLTNGLRIMSVAQEWQIVVTGLIIILAVYGDILRRKK 340


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: 362
Number of extensions: 10
Number of successful extensions: 1
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: 341
Length adjustment: 29
Effective length of query: 318
Effective length of database: 312
Effective search space:    99216
Effective search space used:    99216
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