GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Klebsiella michiganensis M5al

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  384 bits (987), Expect = e-111
 Identities = 216/486 (44%), Positives = 313/486 (64%), Gaps = 4/486 (0%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75
           LR  GI K +    AL N+ F    G+VHALMGENGAGKSTL+KIL G     SG + I 
Sbjct: 10  LRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFID 69

Query: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARF-GLVNRGVLRQQALT 134
            Q +  +   D+   G+A+IHQEL+ VP+MTVAENLFLG  P  F G+++R  + ++A  
Sbjct: 70  GQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHREAKE 129

Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194
            L  +  +IDPQ  +G LS+G++Q+VEIA+A+S  A V+  DEPT++LS  E  +L  +I
Sbjct: 130 KLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLI 189

Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254
            ++R +G  ++Y+SHRMEEV+++ N VTVF+DG ++ T EN+  ++   +V  MVGR I 
Sbjct: 190 AQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGT-ENLGNVSTTDIVRMMVGRQIV 248

Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314
           D+Y + PR  GDV L+V+ L G     PVSF+V  GE++ + GLVG+GRTE+ RLL G +
Sbjct: 249 DLYQHEPRTPGDVLLEVRDLAGSATG-PVSFEVSAGEVVSMSGLVGSGRTEVARLLFGAD 307

Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374
            + +GS+ L  +E +   P  AIA G+ +  EDRK +G+    SV  NI+IS+  +    
Sbjct: 308 PRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNF-VA 366

Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434
           G +++    R    +Q++ L+++       +  LSGGNQQKA L RWL    ++L+LDEP
Sbjct: 367 GGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEP 426

Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494
           TRG+DIGAK EIY++I  LA  G A++V+SSDL E +GISDR+LV+  G +  +L    A
Sbjct: 427 TRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSA 486

Query: 495 NESNLL 500
            E  ++
Sbjct: 487 TEEEVM 492



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 63/227 (27%), Positives = 118/227 (51%), Gaps = 6/227 (2%)

Query: 283 VSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAGVL 342
           V F +  GE+  L G  GAG++ L+++LSG E++  G + +  + + +R+PRDA   G+ 
Sbjct: 28  VRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFIDGQAIDIRTPRDARKYGIA 87

Query: 343 LCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAG 402
           +  ++      +P  +V EN+ +   P+ S  G L R    R   +K  +      P A 
Sbjct: 88  IIHQELNT---VPDMTVAENLFLGQEPT-SFAGILDRKRMHREAKEKLNRINADIDPQA- 142

Query: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIV 462
             +  LS G QQ   + R +S   KVL+LDEPT  +      ++Y++I  +  DG+ ++ 
Sbjct: 143 -PLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLIAQMRQDGVGMVY 201

Query: 463 VSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQRV 509
           +S  + EV  +++R+ V  +G   G  +    + ++++++ + RQ V
Sbjct: 202 ISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQIV 248


Lambda     K      H
   0.320    0.138    0.391 

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: 680
Number of extensions: 27
Number of successful extensions: 9
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: 514
Length of database: 510
Length adjustment: 35
Effective length of query: 479
Effective length of database: 475
Effective search space:   227525
Effective search space used:   227525
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