GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Klebsiella michiganensis M5al

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

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



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  333 bits (854), Expect = 9e-96
 Identities = 179/478 (37%), Positives = 289/478 (60%), Gaps = 8/478 (1%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           LE  G+ K F GV AL  VSL  + G ++ L+GENG GKSTL+K + G   PD+G + ++
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G P      ++AL +GI  ++Q+L+L+P+M+VAEN+ L  E   +        D R LA 
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYG-----FVDHRQLAR 120

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
                L+ + +  +++    L+ +L +A++Q+V IA+A++  A  VIMDEPT++LT+ EV
Sbjct: 121 QTQDLLDKLNIRLSAD---RLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEV 177

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
            +L  ++ +LR QG  ++++SHK+DE +AI  E+ V RDG  +      EFT+  +   M
Sbjct: 178 AHLFTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQM 237

Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315
            GR L+    + +    + VL VR  +R G F D++F +  GEILGV GL+ +GR+E+  
Sbjct: 238 VGRELTQLFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVME 297

Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375
           +L G+  A SG+VL+DG  + + +PS A    +  + EDR   GLFL   + +N+    +
Sbjct: 298 SLFGMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKM 357

Query: 376 SSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 435
                + G +   +      + ++ L I TP +D+ + +LSGGNQQ+VLI RWL   P++
Sbjct: 358 PEYIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKI 417

Query: 436 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493
           LIL  PT G+DVG+K  IY ++  L+ RG+ +I++S +LPE+L   DR+++M +G ++
Sbjct: 418 LILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRIT 475


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: 575
Number of extensions: 24
Number of successful extensions: 5
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: 515
Length of database: 494
Length adjustment: 34
Effective length of query: 481
Effective length of database: 460
Effective search space:   221260
Effective search space used:   221260
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