GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Shewanella amazonensis SB2B

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 6939484 Sama_3576 ATP-binding transport protein NatA (RefSeq)

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__SB2B:6939484
          Length = 244

 Score = 99.4 bits (246), Expect = 6e-26
 Identities = 67/223 (30%), Positives = 117/223 (52%), Gaps = 18/223 (8%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           ++++  ++K  G V+AL+ +S E   GE+  LLG NGAGK+T ++ + G  KPD G+ + 
Sbjct: 1   MIKVNGLYKKIGQVQALNNLSFEARDGEITGLLGPNGAGKTTCLRTLFGLLKPDEGNAII 60

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIF-----LNKKKMM 118
           +G  V    P  A+        Q L L PD    Y     RE   + F     +N +   
Sbjct: 61  DGVDVA-EQPIVAK--------QALGLFPDPFGLYERLTPREYI-RFFAELSGMNGRTAD 110

Query: 119 EESKKLLDSLQIRIPDI-NMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEA 177
           E + ++L   Q+ + DI + + +  S GQR   A+A+A+    + I++DEPT  L V+  
Sbjct: 111 EATSRVL--AQLNMQDIADRRCKGFSQGQRMKTALAQAIVHQPRNIILDEPTRGLDVMST 168

Query: 178 RKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220
           R +  +  +L+ +G  VL  +H + +   + DR+ V+ RG+++
Sbjct: 169 RVLRGMLSDLRAQGHCVLFSSHVMQEVAALCDRVIVMARGEVV 211


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: 117
Number of extensions: 6
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: 244
Length adjustment: 24
Effective length of query: 227
Effective length of database: 220
Effective search space:    49940
Effective search space used:    49940
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: 46 (22.3 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