GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Herbaspirillum seropedicae SmR1

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate HSERO_RS12120 HSERO_RS12120 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__HerbieS:HSERO_RS12120
          Length = 266

 Score =  194 bits (494), Expect = 1e-54
 Identities = 98/250 (39%), Positives = 158/250 (63%), Gaps = 4/250 (1%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           +LE+  V K FG V AL  VS+ + +GEV  LLGDNGAGKSTLIK+++G H+   G  + 
Sbjct: 11  ILELDQVSKFFGPVIALQNVSLRLRRGEVHCLLGDNGAGKSTLIKLLAGVHQASSGQYLV 70

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIF----LNKKKMME 119
           +GK V F SP +A  +G+ T+YQDLAL+P L +  N FL RE   K+F    ++ +    
Sbjct: 71  DGKPVRFESPKEALDVGVATVYQDLALVPLLSVARNFFLGREPVRKLFGVTVMDMELAAR 130

Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179
            +K+ L  + I + D +  +  +SGG++Q +A+ARA++F A+++++DEPTAAL V ++  
Sbjct: 131 TAKEKLAEMGIMVRDAHHPIGTMSGGEKQCLAIARAIHFGARVLILDEPTAALGVKQSFN 190

Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTS 239
           VL+L    +++G+ V+ ITHN+   Y + D   +L+RGK +    K+  + EE+ ++M  
Sbjct: 191 VLKLIHRARERGISVIFITHNVHHAYPIGDTFTLLNRGKSLGSFAKDRISKEEVLDMMAG 250

Query: 240 FALGKVNLGE 249
            A  +  +G+
Sbjct: 251 GAEMQTLMGQ 260


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: 159
Number of extensions: 8
Number of successful extensions: 2
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: 266
Length adjustment: 24
Effective length of query: 227
Effective length of database: 242
Effective search space:    54934
Effective search space used:    54934
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: 47 (22.7 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