GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Dethiosulfovibrio salsuginis USBA 82

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085544740.1 B9Y55_RS07445 sugar ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_900177735.1:WP_085544740.1
          Length = 497

 Score =  159 bits (403), Expect = 8e-44
 Identities = 84/235 (35%), Positives = 146/235 (62%), Gaps = 2/235 (0%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           +E+R++ K FG V ALD V + ++ GE+  L G NG+GKSTLIKIISG ++P+ G  +F 
Sbjct: 8   IELRNISKRFGGVTALDDVGLSLSPGEIHCLAGQNGSGKSTLIKIISGVYRPEDGAEIFI 67

Query: 65  GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREV-TNKIFLNKKKMMEESKK 123
             +++   P  A  +GI+ IYQDL++ P L +  NI L +     + F++K +++ ++K 
Sbjct: 68  DGELVALDPAKAIGIGIQVIYQDLSIFPGLSVAENIGLGQYCEKGRFFVDKGRLVSDAKT 127

Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183
            ++ + I +P +  KV  LS   RQ VA+ RA+   A++++MDEPTA+L+  E + +L +
Sbjct: 128 AMNKIGISLP-LRKKVSELSIADRQLVAICRALANDARLVIMDEPTASLTRTEVKALLSV 186

Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238
            + LK + + V+ ++H + +  EVA+R+ VL  GK +   +  E + +++   MT
Sbjct: 187 VKELKNRDIAVVFVSHRLDEVIEVAERVTVLRDGKSVGVFEASELDDKKLATYMT 241



 Score = 99.8 bits (247), Expect = 1e-25
 Identities = 58/219 (26%), Positives = 114/219 (52%), Gaps = 10/219 (4%)

Query: 23  VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82
           VS E+++GE++ + G  G+G++ L   + G + PD G +  EGK +  +S  D    GI 
Sbjct: 274 VSFELHRGEILGITGLLGSGRTELALSLFGKNPPDSGTIALEGKYLSLSSIRDGIYSGIG 333

Query: 83  TIYQD---LALIPDLPIYYNIFLA-----REVTNKIFLNKKKMMEESKKLLDSLQIRIPD 134
            + +D   L ++ D  I  N  L      +     I   K+  +  S   +  L +++ D
Sbjct: 334 YVSEDRLTLGIVMDQSIRDNSVLTVLDRLKSSFGTIDGTKRDQLVSSS--VQELSVKVSD 391

Query: 135 INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGV 194
           +N+ V  LSGG +Q V +A+ +    K++++D PT  + +   + + ++ ++L  KG+G+
Sbjct: 392 VNLPVRTLSGGNQQKVVLAKWLATKPKVLILDSPTVGVDIAAKKGIYDIVKSLSAKGMGI 451

Query: 195 LIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233
           ++I+  I + Y    RI  + RG+I    +  ET+ +++
Sbjct: 452 IMISDEIPEVYYNCHRIITMQRGRITGEYRPTETSEQDL 490


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: 297
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 251
Length of database: 497
Length adjustment: 29
Effective length of query: 222
Effective length of database: 468
Effective search space:   103896
Effective search space used:   103896
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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