Alignments for a candidate for nupA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Klebsiella michiganensis M5al

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  311 bits (796), Expect = 4e-89
 Identities = 177/496 (35%), Positives = 287/496 (57%), Gaps = 10/496 (2%)

Query: 1   MAQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG 60
           M    +E   I+K F    A D+++L +R G +HAL+GENGAGKSTLM  L G+  P  G
Sbjct: 1   MNAFALEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKG 60

Query: 61  SIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQ 120
           +I++ G  V       + + GI M+HQ   LV   TV ENI LG E +K G +D ++  +
Sbjct: 61  AIRVKGEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLAR 120

Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180
           + + L +K  + +  +  + ++S+ +QQ VEI K +   ADI+I DEPT+ LT SE+  L
Sbjct: 121 QTQDLLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHL 180

Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240
            TI++ L ++GK+II I+HK+DEI ++ D ++V R G  + + + +  T Q L   MVGR
Sbjct: 181 FTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGR 240

Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300
            ++    K      E +L++++L     +G  A   ++  V+ GEI+G+AG+ G G+SE+
Sbjct: 241 ELTQLFPKFNNAIGEEVLTVRNL---SRKG--AFHDINFSVRRGEILGVAGLVGAGRSEV 295

Query: 301 VQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQ 360
           ++++ G+ K  SG + I G  V   S     E  +  + EDR + GL L L++ EN+++ 
Sbjct: 296 MESLFGMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSI- 354

Query: 361 TYYKAP--LSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVD 418
              K P  +   G + + K+ E     ++  +++           SGGNQQK +IAR + 
Sbjct: 355 --VKMPEYIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLL 412

Query: 419 RDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDG 478
             P +LI+ +PTRG+DVGA   I+  +    + G AV++VS EL EIL +SDR+ V+H+G
Sbjct: 413 AQPKILILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEG 472

Query: 479 QIQGIVTPETTNKQEL 494
           +I GI+  E  +++ +
Sbjct: 473 RITGILDKEDADQETI 488



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 56/231 (24%), Positives = 119/231 (51%), Gaps = 8/231 (3%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G+ A+  +SL V+ G +  + G +G G+S L++ + G+ +   G + +KG+ V    T  
Sbjct: 17  GVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEPVQFQDTMD 76

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389
                +  + ++ +   L+  +T+AEN+ L    + P+ + G +++ ++    + L+ + 
Sbjct: 77  ALRSGISMIHQELN---LVPHMTVAENIWLG---REPMKY-GFVDHRQLARQTQDLLDKL 129

Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449
           ++R + + +  +  S  +QQ   IA+ V  + D++I+ +PT  L    + ++   +   R
Sbjct: 130 NIRLSADRLVGE-LSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDLR 188

Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500
            +GKA++ +S ++DEI  ++D I+V  DG   G        +Q L   M G
Sbjct: 189 QQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVG 239


Lambda     K      H
   0.315    0.135    0.363 

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: 563
Number of extensions: 35
Number of successful extensions: 6
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: 510
Length of database: 494
Length adjustment: 34
Effective length of query: 476
Effective length of database: 460
Effective search space:   218960
Effective search space used:   218960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources