GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Shewanella oneidensis MR-1

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__MR1:200449
          Length = 378

 Score =  177 bits (448), Expect = 6e-49
 Identities = 95/227 (41%), Positives = 140/227 (61%), Gaps = 6/227 (2%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           V D SL I +GEIF ++G SGSGKST++R+L     PT G++ +DG DI  +   E    
Sbjct: 36  VDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLDGEDITDLPPYE---- 91

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPD 163
             + I M+FQS+AL PHMTV  N AFG++   +   E  ++  + L+ V +E Y    P 
Sbjct: 92  --RPINMMFQSYALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPH 149

Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223
           +LSGG RQRV LAR+LA  P +LL+DE   ALD  +RT+MQ E+V++  +   T V ++H
Sbjct: 150 QLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTH 209

Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDI 270
           D +EAM +  RI+IM +G + Q G+P +I  +P +  +  F   V++
Sbjct: 210 DQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIGSVNL 256


Lambda     K      H
   0.319    0.137    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: 332
Number of extensions: 15
Number of successful extensions: 2
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: 400
Length of database: 378
Length adjustment: 30
Effective length of query: 370
Effective length of database: 348
Effective search space:   128760
Effective search space used:   128760
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 (21.7 bits)
S2: 50 (23.9 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