GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter related (characterized, see rationale)
to candidate H281DRAFT_02174 H281DRAFT_02174 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Burk376:H281DRAFT_02174
          Length = 550

 Score =  442 bits (1138), Expect = e-128
 Identities = 227/498 (45%), Positives = 337/498 (67%), Gaps = 1/498 (0%)

Query: 3   LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62
           L+LE++ I   + GV AL   +L + AGEVHAL+G+NGAGKST++K++TGA  +  G + 
Sbjct: 23  LLLEMQDIGISFGGVPALRGANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGSVR 82

Query: 63  FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADAR 122
           F G    F TP  A++AGIST+YQE+NLVP  +VA+N+FLG EPRR GLI ++ +   A 
Sbjct: 83  FEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWRTVQHRAA 142

Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
           A+L  F L IDV  P+  YS A+QQ++A+AR V+  AK++++DE T+SLD +EV++LF +
Sbjct: 143 ALLDSFGLHIDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELLFTV 202

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           + +L+  G A++F++H LD++Y + DR+TV+R+GQ + +   AE+ + +L+  MLGR+L 
Sbjct: 203 VRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMAEMDKLQLVTTMLGRTLA 262

Query: 243 EQL-VDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301
             +  D   +E  + R     ++  D+     +  ++L V  G+AVGLAGLLGSGR+E  
Sbjct: 263 AVVHDDPAAREANLARRGKQAIAARDLGAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETM 322

Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361
             +FG D ++ GS+ + G  + L  P DAI+ G+A   EDRK +GI+  LS+R+N+ L  
Sbjct: 323 RLMFGADPLERGSVSIDGATVTLKSPQDAIARGLAYLTEDRKAEGIVPELSVRDNLTLVC 382

Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421
              +     +   +QQ I   FI  L I    AD+PI +LSGGNQQKV+LARWLA EP L
Sbjct: 383 LRTLTRNGIVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAEPSL 442

Query: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481
           L+LDEPTRGID+GA A++ K++R L D G+++L+++SEL+EL A S++ VV+RD   V E
Sbjct: 443 LLLDEPTRGIDVGAKADVAKIVRELRDAGLAVLMSASELEELTAVSDRAVVIRDGRTVAE 502

Query: 482 LSGAELTSQHVMQAIAEG 499
           L+GAE++   +M AIA G
Sbjct: 503 LNGAEMSESAIMDAIAYG 520


Lambda     K      H
   0.319    0.136    0.377 

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: 663
Number of extensions: 36
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 499
Length of database: 550
Length adjustment: 35
Effective length of query: 464
Effective length of database: 515
Effective search space:   238960
Effective search space used:   238960
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 (21.8 bits)
S2: 52 (24.6 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