GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS14860 BWI76_RS14860 ABC
           transporter
          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 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