GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Shewanella loihica PV-4

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__PV4:5210736
          Length = 241

 Score =  115 bits (287), Expect = 1e-30
 Identities = 68/221 (30%), Positives = 129/221 (58%), Gaps = 10/221 (4%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           +++I ++HK FG  + L G+   I +GEVV+++G +G+GKST ++ I+   +P +G++V 
Sbjct: 1   MIKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVI 60

Query: 64  EGKKVIFNSPN---DARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120
           +G+ +   +P+   D     +  ++Q+  L P   +  NI LA        + + +   E
Sbjct: 61  DGQSI--TAPDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLG--LMTQAEADSE 116

Query: 121 SKKLLDSLQIRIPD-INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179
           + +LLD  Q+ + D  +    +LSGGQ+Q VA+ARA+    +++L DEPT+AL       
Sbjct: 117 AMRLLD--QVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGD 174

Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220
           VL++ + L + G+ ++I+TH +    +V+DR+  +D G ++
Sbjct: 175 VLDVMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVV 215


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: 122
Number of extensions: 4
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: 241
Length adjustment: 24
Effective length of query: 227
Effective length of database: 217
Effective search space:    49259
Effective search space used:    49259
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.

Links

Downloads

Related tools

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