GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Sphingomonas koreensis DSMZ 15582

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__Korea:Ga0059261_2703
          Length = 313

 Score =  113 bits (283), Expect = 4e-30
 Identities = 75/230 (32%), Positives = 129/230 (56%), Gaps = 13/230 (5%)

Query: 1   MSDLLEIRDVHKSFGAV-KALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRG 59
           M  +L +R V K++ +  KAL  V ++INKGE+ ALLG NGAGK+TLI II G   P  G
Sbjct: 1   MQPILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSG 60

Query: 60  DLVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKK--M 117
            +V +G   I + P  AR + I  + Q+L++     ++  +      + ++F        
Sbjct: 61  TIVVDGHDAI-SEPRAAR-MKIGLVPQELSV----DMFETVQATTRYSRRLFGRPANDAY 114

Query: 118 MEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEA 177
           +++  K L     R    N KV  LSGG ++ V +A+A+     ++ +DEPTA + V   
Sbjct: 115 IDQVLKDLSLYDKR----NSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLR 170

Query: 178 RKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEE 227
           R + +L  +L+++G  +++ TH I +  E+ADR+ V+++G+++  + K E
Sbjct: 171 RDMWKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGELLLVEGKAE 220


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: 162
Number of extensions: 9
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: 313
Length adjustment: 26
Effective length of query: 225
Effective length of database: 287
Effective search space:    64575
Effective search space used:    64575
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