GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ytfR in Klebsiella michiganensis M5al

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS14860 BWI76_RS14860 ABC
           transporter
          Length = 510

 Score =  360 bits (925), Expect = e-104
 Identities = 198/491 (40%), Positives = 296/491 (60%), Gaps = 11/491 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +LR EG+SK +    AL+NV F L  GE+ AL+GENGAGKSTL+K L+G    D G I++
Sbjct: 9   LLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFI 68

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRF-GLLRRKEMEKRAT 127
           +GQAI  +    A++ GI  ++QE+N +P+M+VA+NLF+G+EP  F G+L RK M + A 
Sbjct: 69  DGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHREAK 128

Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
           E +      +D + PL   S+  QQ+V I RA+  +AKVL+LDEPTA+L   E   L+ L
Sbjct: 129 EKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRL 188

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR--- 244
           + Q+R  GV +++++H +++V+Q+++R+TV R+G+++G      +   ++V+MM+GR   
Sbjct: 189 IAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQIV 248

Query: 245 ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304
           +L  H  +  G  LL  + +A            P   EV  GE+V ++GL+GSGRTE A 
Sbjct: 249 DLYQHEPRTPGDVLLEVRDLAG-------SATGPVSFEVSAGEVVSMSGLVGSGRTEVAR 301

Query: 305 VIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ 364
           ++FG  P   G+  + G+      P  A   GIG   EDRKT G+    SV  NI ++  
Sbjct: 302 LLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSL 361

Query: 365 AQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424
                   + RK  +      +R+L +R  + E P+  LSGGNQQK  L+RWLL   + L
Sbjct: 362 DNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLL 421

Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEI 484
           ILDEPTRG+D+GA  EI  LI+ L   G A+LVISS+L E +G +DRV++MR  + V ++
Sbjct: 422 ILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQL 481

Query: 485 PLAELSVPAIM 495
           P    +   +M
Sbjct: 482 PSCSATEEEVM 492


Lambda     K      H
   0.321    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: 584
Number of extensions: 26
Number of successful extensions: 8
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: 500
Length of database: 510
Length adjustment: 34
Effective length of query: 466
Effective length of database: 476
Effective search space:   221816
Effective search space used:   221816
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