GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylGsa in Pseudomonas fluorescens GW456-L13

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:P0DTT6
         (251 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  127 bits (318), Expect = 6e-34
 Identities = 72/216 (33%), Positives = 122/216 (56%), Gaps = 1/216 (0%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           L    + K+F  VKALD +S   + G+V AL+G+NGAGKSTL+KI+ G + P  G L   
Sbjct: 16  LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75

Query: 65  GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKL 124
            + + F S  D+   G+  I+Q+L L+P++ +  N+FL     +   +N+  + +++   
Sbjct: 76  ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALAC 135

Query: 125 LDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELA 184
           L  L   I D   KV  LS GQRQ V +A+A+   A +I  DEPT++LS  E  +++ + 
Sbjct: 136 LKGLADEI-DPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194

Query: 185 RNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220
             L+ +G  VL ++H + + + + + + V   G+ +
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYV 230



 Score =  101 bits (252), Expect = 3e-26
 Identities = 56/220 (25%), Positives = 118/220 (53%), Gaps = 6/220 (2%)

Query: 23  VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82
           VS E++KGE++ L G  GAG++ L++++SG  +   G L   G ++   SP DA + GI 
Sbjct: 283 VSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGIL 342

Query: 83  TIYQDL---ALIPDLPIYYNIFLAREVTNKIF---LNKKKMMEESKKLLDSLQIRIPDIN 136
              +D     ++P   +  NI ++    +  F   L      + +++ + +L+++ P+  
Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAA 402

Query: 137 MKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGVLI 196
            K+  LSGG +Q   + R +    K++L+DEPT  + +    ++ ++  NL  +G+ V++
Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIV 462

Query: 197 ITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEV 236
           ++ ++++   ++DRI VL  G +     +E+ N   + ++
Sbjct: 463 VSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQL 502


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: 260
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: 514
Length adjustment: 29
Effective length of query: 222
Effective length of database: 485
Effective search space:   107670
Effective search space used:   107670
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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