GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Shewanella loihica PV-4

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 5209155 Shew_1633 lipoprotein releasing system, ATP-binding protein (RefSeq)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__PV4:5209155
          Length = 233

 Score =  100 bits (248), Expect = 3e-26
 Identities = 70/220 (31%), Positives = 114/220 (51%), Gaps = 10/220 (4%)

Query: 1   MLSFDKVSTYY--GKI--QALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASG 56
           +L    VS  Y  G I  Q L  V++ + KGE V +IG++G+GKSTLL  +    + +SG
Sbjct: 9   LLQVSNVSKRYHEGSIDTQVLSGVNLSIAKGEQVAIIGSSGSGKSTLLHIMGTLDKPSSG 68

Query: 57  SIRYEGEELVGLPSS---TIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQM 113
            + ++GE+L  L  S    I  + +  + +   +    T  EN+AM G    +   +V+ 
Sbjct: 69  QVMFDGEDLYQLSPSRQAAIRNQELGFIYQFHHLLPEFTALENVAMPGLIQKRPRQEVEQ 128

Query: 114 DKVLELFPR--LKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQ 171
           +   EL  R  L  R       MSGGE+Q  AI RAL+++PKL+L DEP+  L       
Sbjct: 129 E-AKELLSRVGLGHRLHHTPAEMSGGERQRTAIARALINRPKLVLADEPTGNLDAASGDS 187

Query: 172 IFEIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRI 211
           ++E+I +L  +  T F+V  +  +     DR   +++G++
Sbjct: 188 VYELIRELGSQLGTAFVVVTHDPKLAARMDRQLKMQDGQL 227


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: 126
Number of extensions: 2
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: 233
Length adjustment: 23
Effective length of query: 210
Effective length of database: 210
Effective search space:    44100
Effective search space used:    44100
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