GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylK_Tm in Dechlorosoma suillum PS

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:Q9WXX0
         (520 letters)



>lcl|FitnessBrowser__PS:Dsui_0627 Dsui_0627 ABC-type branched-chain
           amino acid transport systems, ATPase component
          Length = 267

 Score =  131 bits (329), Expect = 3e-35
 Identities = 83/267 (31%), Positives = 138/267 (51%), Gaps = 9/267 (3%)

Query: 10  DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69
           +R  +L+A  + K F GV A+  V   + E EI  LIG NGAGK+T    LTG+  P+ G
Sbjct: 3   ERPILLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGG 62

Query: 70  EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLA-YEAVRGQK-----RT 123
            I+  G  ++  +P     +GI+   Q + L  +MT  EN+ +  ++  R        RT
Sbjct: 63  RIVFAGAELDTSAPHKVAARGIARTFQNIRLFAHMTALENVMVGRHQRTRAGVFGAIFRT 122

Query: 124 LSSRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEP 183
             +R +E  +  R++ELL  +G       L ++L+   ++ +EI +AL  EP+++ +DEP
Sbjct: 123 PGTRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKLLALDEP 182

Query: 184 TSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEF 243
            + +   ET  L  +IE ++  GI+V+ + H +  VM + DR+ V+  G++I E      
Sbjct: 183 AAGMNASETGELRTLIEGIRKDGITVLLIEHDVKLVMGLCDRVAVLDYGEKICEDVPAVV 242

Query: 244 DVD-TIIKMMVGREVEFFPHGIETRPG 269
             D  +I   +G E +  P G E   G
Sbjct: 243 QKDPRVITAYLGAEAQ--PAGSEVAHG 267



 Score = 72.0 bits (175), Expect = 2e-17
 Identities = 50/214 (23%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 284 VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKM 343
           ++ VS  +R+GE+ G  G  GAG+T     + G+     G I   G +++   P      
Sbjct: 23  LRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVFAGAELDTSAPHKVAAR 82

Query: 344 GIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRW---------GLVLDERKEEEISEDY 394
           GI    ++ +L      MT  +N+++   ++             G   +E   +  +E+ 
Sbjct: 83  GIARTFQNIRL---FAHMTALENVMVGRHQRTRAGVFGAIFRTPGTRAEEAAIQRRAEEL 139

Query: 395 VKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMI 454
           +  + I   + + + ++LS G+Q+++ +A+ LAT   +L  DEP  G++     E+  +I
Sbjct: 140 LHYVGIADRA-HDLAKHLSYGDQRRLEIARALATEPKLLALDEPAAGMNASETGELRTLI 198

Query: 455 RELAAQGKAVIMISSELPEILNLSDRIVVMWEGE 488
             +   G  V++I  ++  ++ L DR+ V+  GE
Sbjct: 199 EGIRKDGITVLLIEHDVKLVMGLCDRVAVLDYGE 232


Lambda     K      H
   0.319    0.138    0.381 

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: 300
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: 520
Length of database: 267
Length adjustment: 30
Effective length of query: 490
Effective length of database: 237
Effective search space:   116130
Effective search space used:   116130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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, the preprint on GapMind for carbon sources, 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