GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Dinoroseobacter shibae DFL-12

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 3608244 Dshi_1648 ABC transporter related (RefSeq)

Query= reanno::Smeli:SMc02121
         (258 letters)



>FitnessBrowser__Dino:3608244
          Length = 373

 Score =  148 bits (374), Expect = 1e-40
 Identities = 87/238 (36%), Positives = 137/238 (57%), Gaps = 9/238 (3%)

Query: 19  IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78
           +++T + K YGD  VL +INL + +GE IV  GPSG GKST++R I  LE+   G + +D
Sbjct: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63

Query: 79  GIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFL 138
           G  + ND   +   +R + MVFQ + L+PH+T+ EN + A + + K  + E +       
Sbjct: 64  G-TVVND---VPPAQRGIAMVFQSYALYPHMTVRENMSFA-LKIAKKSQAEIDAAVEAAA 118

Query: 139 ERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVG 198
           E++++ +   + P  LSGGQ+QRVAI RS+   PK+ LFDEP S LD  + +      + 
Sbjct: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAAL-RVATRLEIA 177

Query: 199 LAEEGM---TMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFL 253
             +E M   TM+ VTH+   A  +A R++ +  G I +  SP E ++ P++E    F+
Sbjct: 178 QLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235


Lambda     K      H
   0.322    0.136    0.397 

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: 235
Number of extensions: 8
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: 258
Length of database: 373
Length adjustment: 27
Effective length of query: 231
Effective length of database: 346
Effective search space:    79926
Effective search space used:    79926
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 (21.9 bits)
S2: 48 (23.1 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