GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Acidovorax sp. GW101-3H11

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  315 bits (807), Expect = 2e-90
 Identities = 186/496 (37%), Positives = 289/496 (58%), Gaps = 17/496 (3%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           +E   V K F  V  L GV  + Q G++Y LLGENG GKSTL+KI++G + P  G++V++
Sbjct: 5   VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64

Query: 76  GVPHARLSALEALAA-GIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLA 134
           G   A      A  A GI  ++Q+ +L  ++++A+N+ L      HE +     D + + 
Sbjct: 65  GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLG-----HEIKRGLFLDDKAMR 119

Query: 135 ATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKE 194
                AL  VGLP + +   T + +L +A +QLV IARA+A  A+ +IMDEPT +LT  E
Sbjct: 120 EKTREALAKVGLPLDPD---TRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGE 176

Query: 195 VDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISEL 254
            + L A++A L+A GVT++++SHKLDE      EV+V+RDG  +A+   A  T+ Q++ L
Sbjct: 177 TERLFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANL 236

Query: 255 MTGRHLSNERYRESAHAQD--IVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNE 312
           M GR L++    +    QD    + VRG T  G    V F++  GEILG  GL+ +GR E
Sbjct: 237 MVGRELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTE 296

Query: 313 LARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVIT 372
           L   L G+ P  +G V + GQ + L++P DA RH + Y+ EDR  +GL +   +R N+  
Sbjct: 297 LFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTL 356

Query: 373 AMISSLRDRFGQ--IDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLA 430
             +    +R+ +  +D    QA   + V+E  I T  ++    SLSGGNQQ++ + + L 
Sbjct: 357 MAL----ERYAKPWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLH 412

Query: 431 IDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKG 490
             P V++L  PT GVDVG+K  IY ++QRL+++G+ +I+IS +L EL+  C R+ +M+ G
Sbjct: 413 PGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAG 472

Query: 491 HVSAEYRADELSEADL 506
            +    +   L+E +L
Sbjct: 473 RLQTTLQEPHLTEEEL 488



 Score = 52.0 bits (123), Expect = 5e-11
 Identities = 55/236 (23%), Positives = 101/236 (42%), Gaps = 25/236 (10%)

Query: 33  GVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGI 92
           GV    +RG+I    G  G G++ L + + G +P   G + I G P    S  +A   G+
Sbjct: 273 GVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGL 332

Query: 93  ETVYQD---------LSLLPNMSVAENVALTSELATHEGRLARTF-DRRVLAATAARALE 142
             + +D           L PN+++   +AL         R A+ + D     A    A++
Sbjct: 333 TYLSEDRKGKGLHVHFGLRPNLTL---MALE--------RYAKPWLDPAAEQAALREAVQ 381

Query: 143 AVGL-PGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAV 201
             G+  G+ E +++    L    +Q +A+A+ +      V++DEPT  +       +  +
Sbjct: 382 EFGIRTGSLEVRAS---SLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHL 438

Query: 202 LANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
           +  L  QG+ V+ +S +L E   +   V V+R G+          T+ ++    TG
Sbjct: 439 VQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATG 494


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: 568
Number of extensions: 32
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: 496
Length adjustment: 34
Effective length of query: 481
Effective length of database: 462
Effective search space:   222222
Effective search space used:   222222
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