GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Paraburkholderia bryophila 376MFSha3.1

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate H281DRAFT_02174 H281DRAFT_02174 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Burk376:H281DRAFT_02174
          Length = 550

 Score =  323 bits (828), Expect = 1e-92
 Identities = 196/516 (37%), Positives = 302/516 (58%), Gaps = 25/516 (4%)

Query: 7   SSAPLSQPFL-EVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65
           S +P ++P L E+  +   F GV ALRG +LS   G+++ L+G+NG GKST+IKI++GA 
Sbjct: 15  SQSPATRPLLLEMQDIGISFGGVPALRGANLSVAAGEVHALIGQNGAGKSTMIKILTGAY 74

Query: 66  PPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA 125
               G +  EG      +  +A  AGI T+YQ+++L+P  SVAEN+ L        GR  
Sbjct: 75  RRGSGSVRFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFL--------GREP 126

Query: 126 RTF---DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVI 182
           R F   D R +   AA  L++ GL  + +     + +   A +Q+VA+ARA++S+AK VI
Sbjct: 127 RRFGLIDWRTVQHRAAALLDSFGLHIDVKKP---VGRYSTAIQQMVALARAVSSDAKMVI 183

Query: 183 MDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGP 242
           MDE T+SL ++EV+ L  V+  LR  G  V+FVSH+LDE YA+   V V+RDGQ +AQ  
Sbjct: 184 MDESTSSLDEREVELLFTVVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQST 243

Query: 243 IAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAG--------QFSDVSFKL 294
           +AE  K Q+   M GR L+   + + A A++  L  RG             + SDVS ++
Sbjct: 244 MAEMDKLQLVTTMLGRTLAAVVHDDPA-AREANLARRGKQAIAARDLGAHPKVSDVSLEV 302

Query: 295 HGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPED 354
           H GE +G+ GLL SGR E  R + G  P + G V +DG  + L++P DA    + Y+ ED
Sbjct: 303 HAGEAVGLAGLLGSGRTETMRLMFGADPLERGSVSIDGATVTLKSPQDAIARGLAYLTED 362

Query: 355 RLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQS 414
           R  EG+  +  +RDN+    + +L  R G +D  + QA+ ++ +  L I     D+P++ 
Sbjct: 363 RKAEGIVPELSVRDNLTLVCLRTL-TRNGIVDVKKQQAIVDRFIASLGIKLRSADQPIRE 421

Query: 415 LSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDL 474
           LSGGNQQ+VL+ RWLA +P +L+L  PT G+DVG+K  + +I++ L   G+ +++ + +L
Sbjct: 422 LSGGNQQKVLLARWLAAEPSLLLLDEPTRGIDVGAKADVAKIVRELRDAGLAVLMSASEL 481

Query: 475 PELLQNCDRILMMKKGHVSAEYRADELSEADLYHAL 510
            EL    DR ++++ G   AE    E+SE+ +  A+
Sbjct: 482 EELTAVSDRAVVIRDGRTVAELNGAEMSESAIMDAI 517



 Score = 84.7 bits (208), Expect = 8e-21
 Identities = 66/251 (26%), Positives = 124/251 (49%), Gaps = 11/251 (4%)

Query: 24  RFTGVHA-LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARL 82
           R  G H  +  VSL    G+   L G  G G++  ++++ GA P + G + I+G      
Sbjct: 287 RDLGAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETMRLMFGADPLERGSVSIDGATVTLK 346

Query: 83  SALEALAAGIETVYQDLS---LLPNMSVAENVALTS-ELATHEGRLARTFDRRVLAATAA 138
           S  +A+A G+  + +D     ++P +SV +N+ L      T  G +    D +   A   
Sbjct: 347 SPQDAIARGLAYLTEDRKAEGIVPELSVRDNLTLVCLRTLTRNGIV----DVKKQQAIVD 402

Query: 139 RALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNL 198
           R + ++G+   S  Q   I +L    +Q V +AR +A+E   +++DEPT  +      ++
Sbjct: 403 RFIASLGIKLRSADQP--IRELSGGNQQKVLLARWLAAEPSLLLLDEPTRGIDVGAKADV 460

Query: 199 IAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGR 258
             ++  LR  G+ VL  + +L+E  A+    +V+RDG+ +A+   AE +++ I + +   
Sbjct: 461 AKIVRELRDAGLAVLMSASELEELTAVSDRAVVIRDGRTVAELNGAEMSESAIMDAIAYG 520

Query: 259 HLSNERYRESA 269
             S+ +  E+A
Sbjct: 521 GDSSSQLAEAA 531


Lambda     K      H
   0.319    0.135    0.376 

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: 633
Number of extensions: 31
Number of successful extensions: 7
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: 515
Length of database: 550
Length adjustment: 35
Effective length of query: 480
Effective length of database: 515
Effective search space:   247200
Effective search space used:   247200
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: 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