GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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