GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pedobacter sp. GW460-11-11-14-LB5

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Pedo557:CA265_RS04345
          Length = 216

 Score =  107 bits (266), Expect = 2e-28
 Identities = 72/217 (33%), Positives = 116/217 (53%), Gaps = 6/217 (2%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           ML    +   YG +Q L  V+ EV+KGEIV++IG +GAGKSTLL  L    +   GS++ 
Sbjct: 1   MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL 60

Query: 61  EG---EELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF--TDKDDYQVQMDK 115
           +G    +L G   ST   ++I  V +   +    +  EN+ +  F   T+K   + +  +
Sbjct: 61  KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFE 120

Query: 116 VLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEI 175
           +L+LF  LK+R + +   +SGGEQQ +AI RAL++ P ++L DEPS  L       + ++
Sbjct: 121 LLDLFG-LKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQL 179

Query: 176 IEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIV 212
              LR      F++  +     K +DR   +++G IV
Sbjct: 180 FVSLRDNFHQTFVIVTHNEHLAKTSDRVVSMKDGLIV 216


Lambda     K      H
   0.318    0.136    0.374 

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: 104
Number of extensions: 4
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: 233
Length of database: 216
Length adjustment: 22
Effective length of query: 211
Effective length of database: 194
Effective search space:    40934
Effective search space used:    40934
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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