GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Klebsiella michiganensis M5al

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__Koxy:BWI76_RS19640
          Length = 506

 Score =  162 bits (411), Expect = 1e-44
 Identities = 82/241 (34%), Positives = 154/241 (63%), Gaps = 1/241 (0%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           LLE+ +++KSF  VKALD V++++    + AL+G+NGAGKSTL+K + G ++ D G ++F
Sbjct: 13  LLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSILF 72

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123
           +G+++ F+S  +A   GI  ++Q+L L+    +  N++L R  T  +F+++ KM  ++K 
Sbjct: 73  QGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGVFVDQDKMYRDTKA 132

Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183
           + D L I I D   +V  LS  Q Q + +A+A  ++AK+++MDEPT++L+  E   + ++
Sbjct: 133 IFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFKI 191

Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFALG 243
            R LK++G G++ I+H + + +++ D I +L  G+ I  +  E  ++++I  +M   +L 
Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLN 251

Query: 244 K 244
           +
Sbjct: 252 Q 252



 Score = 92.8 bits (229), Expect = 1e-23
 Identities = 53/217 (24%), Positives = 119/217 (54%), Gaps = 6/217 (2%)

Query: 23  VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82
           +S +++KGE++ + G  GA ++ +++ + G  +   G +   GKK+  +S N+A + G  
Sbjct: 282 ISFDLHKGEILGIAGLVGAKRTDIVETLFGIREKAGGTIRLHGKKINNHSANEAINHGFA 341

Query: 83  TIYQD---LALIPDLPIYYNIFLA--REVTNKI-FLNKKKMMEESKKLLDSLQIRIPDIN 136
            + ++     +   L I +N  ++  ++  NK+  L+  +M  +++ ++DS++++ P  +
Sbjct: 342 LVTEERRSTGIYAYLDIGFNSLISNIKKYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGQH 401

Query: 137 MKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGVLI 196
            ++ +LSGG +Q V + R +    +++++DEPT  + V    ++ +L   L KK  G++I
Sbjct: 402 TQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKDKGIII 461

Query: 197 ITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233
           I+  + +   + DRI V+  G +    + + T   EI
Sbjct: 462 ISSEMPELLGITDRILVMSNGLVAGIVETKTTTQNEI 498


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: 273
Number of extensions: 12
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: 506
Length adjustment: 29
Effective length of query: 222
Effective length of database: 477
Effective search space:   105894
Effective search space used:   105894
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 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