GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Dechlorosoma suillum PS

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  118 bits (295), Expect = 2e-31
 Identities = 82/252 (32%), Positives = 135/252 (53%), Gaps = 13/252 (5%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           +EIR++ K FG   ALD VS+ I  GE+VALLG +G GK+TL++II+G    D G ++FE
Sbjct: 3   IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62

Query: 65  GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEES--K 122
           G +    +   AR   +  ++Q  AL   + ++ N+     V  +    K++  E    K
Sbjct: 63  GSEA---THLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPR----KERPCESEIRK 115

Query: 123 KLLDSLQIRIPD--INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180
           +++D L +   D   +     LSGGQRQ +A+ARA+    K++L+DEP  AL     +++
Sbjct: 116 RVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKEL 175

Query: 181 LELARNL-KKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTS 239
               R L  +  +  + +TH+  +  EVADR+ V+++G+I      +E      +  +  
Sbjct: 176 RRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQ 235

Query: 240 FALGKVNLGEKR 251
           F LG VN+   R
Sbjct: 236 F-LGNVNVFHSR 246


Lambda     K      H
   0.318    0.137    0.371 

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: 149
Number of extensions: 9
Number of successful extensions: 3
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: 251
Length of database: 360
Length adjustment: 27
Effective length of query: 224
Effective length of database: 333
Effective search space:    74592
Effective search space used:    74592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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