GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Dyella japonica UNC79MFTsu3.2

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  150 bits (380), Expect = 4e-41
 Identities = 79/216 (36%), Positives = 139/216 (64%), Gaps = 3/216 (1%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           +L+ R + K FGA  ALDGV + +  GEV AL+G NGAGKSTLIK+++G  +PDRG +  
Sbjct: 12  VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK--IFLNKKKMMEES 121
           +G+ +  ++P +A+  GI T+YQ++ L P+L +  N++  R    +    ++ +++ + +
Sbjct: 72  DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131

Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181
           + LL  L + + D++  + +     RQ VA+ARA+  SA+++++DEPT++L   E R++ 
Sbjct: 132 RSLLRQLHLEL-DVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190

Query: 182 ELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRG 217
            +   L+++G+ +L +TH + Q Y V+DRI VL  G
Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDG 226



 Score = 80.1 bits (196), Expect = 8e-20
 Identities = 53/207 (25%), Positives = 106/207 (51%), Gaps = 4/207 (1%)

Query: 12  KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71
           +  G    L  V +++ +GE++ L G  G+G++ L +++ G  + +RG+L   G++V   
Sbjct: 274 QGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELK 333

Query: 72  SPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKIF-LNKKKMMEESKKLLDS 127
            P DA   G+    ++     ++ +L +  NI LA +       +++ +  E +++L+ +
Sbjct: 334 HPADAVVRGLALCPEERKTDGIVAELSVRENIVLALQARQGWRGMSRARQDELARQLVQA 393

Query: 128 LQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNL 187
           L I+  DI   V  LSGG +Q V +AR +    +++++DEPT  + V   ++++      
Sbjct: 394 LGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRR 453

Query: 188 KKKGLGVLIITHNIIQGYEVADRIYVL 214
              G+ VL I+    +     DRI V+
Sbjct: 454 AHAGMAVLFISAETGELTRWCDRIAVM 480


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: 262
Number of extensions: 14
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: 505
Length adjustment: 29
Effective length of query: 222
Effective length of database: 476
Effective search space:   105672
Effective search space used:   105672
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