GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= uniprot:A0A159ZWL6
         (233 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  117 bits (294), Expect = 2e-31
 Identities = 72/230 (31%), Positives = 125/230 (54%), Gaps = 11/230 (4%)

Query: 2   LQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYM 61
           +  + V+  +G   A+ SVN+E++ GE+  L+G +G+GK+TLL  + G  QA SG +++ 
Sbjct: 3   IHIQQVNKHFGNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVKFN 62

Query: 62  GEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMG------GFFTDKGDYQEQMDK 115
           GE++  Q   H+  + +  V +   +F  +TV EN+A G           K +  E++  
Sbjct: 63  GEDITTQ---HVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHS 119

Query: 116 VLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDI 175
           +L L  +L     +    +SGG++Q +A+ RAL  +PK+LLLDEP   L   +  ++   
Sbjct: 120 LLKLV-QLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRW 178

Query: 176 IEQLRKD-GVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDP 224
           + +L  +  VT   V  +  +AL++AD+  V+  GR+  QGT E +   P
Sbjct: 179 LRRLHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTP 228


Lambda     K      H
   0.320    0.137    0.381 

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: 197
Number of extensions: 9
Number of successful extensions: 4
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: 354
Length adjustment: 26
Effective length of query: 207
Effective length of database: 328
Effective search space:    67896
Effective search space used:    67896
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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