GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Klebsiella michiganensis M5al

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  441 bits (1135), Expect = e-128
 Identities = 237/500 (47%), Positives = 325/500 (65%), Gaps = 5/500 (1%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           ++  PLL++ GI K +GATLAL+++   +  GE+HALMGENGAGKSTLMK+LSG    D 
Sbjct: 4   ISSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDS 63

Query: 61  GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120
           G I +DG+ + +R P  +R  GI +I+QEL   P+++VA N+F+G E  +  G++D   M
Sbjct: 64  GVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRM 123

Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
                  L ++ A        G LSI  QQ VEIARA+   ++++++DEPTAALS  ET 
Sbjct: 124 HREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETL 183

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
           QL+ ++ ++R +G+ ++YISHRM EV+ LA+RVTV RDG+++G      + +  IV+MMV
Sbjct: 184 QLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMV 243

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300
           GR + + YQH+   P D      +++VR LAG    P SF+V AGEV+  +GLVG+GRTE
Sbjct: 244 GRQIVDLYQHEPRTPGD-----VLLEVRDLAGSATGPVSFEVSAGEVVSMSGLVGSGRTE 298

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360
           +ARLLFGADPRS G + L GR      P AA+  GI  V EDRK QGLFL  +V  N  +
Sbjct: 299 VARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDI 358

Query: 361 NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420
           +        G+V+ +++       ++RL ++    E PV  LSGGNQQK  LARWL    
Sbjct: 359 SSLDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDS 418

Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480
           ++LILDEPTRGVDI AK EIY+L+ RLA  G A++VISS+LPE IGI DRVLVMR G I 
Sbjct: 419 RLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIV 478

Query: 481 GELAGAAITQENIMRLATDT 500
            +L   + T+E +M  AT T
Sbjct: 479 HQLPSCSATEEEVMLHATGT 498



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 24/253 (9%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL++R +  S     A   +   +  GE+ ++ G  G+G++ + ++L G     QG + L
Sbjct: 262 LLEVRDLAGS-----ATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRL 316

Query: 66  DGRPVALRDPGASRAAGINLIYQEL---------AVAPNISVAA--NVFMGSELRTRLGL 114
            GR     DP A+ A GI ++ ++          +V  NI +++  N   G       G+
Sbjct: 317 AGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFVAG-------GV 369

Query: 115 IDHAAMRSRTDAVLRQLGAGFGASDL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAA 173
           +    +R+     +R+L     A +L    LS   QQ+  +AR L+  SR++I+DEPT  
Sbjct: 370 VKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRG 429

Query: 174 LSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSE 233
           +      +++ ++ RL   G AI+ IS  + E   ++DRV V+R G  V +L       E
Sbjct: 430 VDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEE 489

Query: 234 RIVQMMVGRSLSE 246
            ++    G   S+
Sbjct: 490 EVMLHATGTFTSQ 502


Lambda     K      H
   0.320    0.135    0.378 

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: 752
Number of extensions: 27
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: 521
Length of database: 510
Length adjustment: 35
Effective length of query: 486
Effective length of database: 475
Effective search space:   230850
Effective search space used:   230850
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 (21.8 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