GapMind for catabolism of small carbon sources

 

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

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate 3608990 Dshi_2380 ABC transporter related (RefSeq)

Query= TCDB::P0AAG3
         (241 letters)



>FitnessBrowser__Dino:3608990
          Length = 257

 Score =  148 bits (373), Expect = 1e-40
 Identities = 90/217 (41%), Positives = 134/217 (61%), Gaps = 5/217 (2%)

Query: 1   MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60
           MI L+ VSK +G  +VL      + KGE +V+ G SG+GKS ++K+V GL     G+I V
Sbjct: 10  MIELRGVSKAFGPKEVLRGVDLVIPKGESMVIIGGSGTGKSVMLKSVLGLISPDAGQILV 69

Query: 61  DGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVK-VLKRDKAPAREKALK 119
           DG  V  +K +     +R GM+FQ   LF  L + +N++   ++  LKR +A AR+ A++
Sbjct: 70  DGKDV--EKVERDAFLARFGMLFQGGALFDSLPVWQNVSFRLLRGALKRPRAEARDIAIE 127

Query: 120 LLERVGLSAH-ANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDV 178
            L RVGL+   A++FPA+LSGG Q+RV +ARA+  +P  + FDEPT+ LDP M   + D+
Sbjct: 128 KLRRVGLTPDVADQFPAELSGGMQKRVGLARAIAAEPEIIFFDEPTTGLDPIMSGVINDL 187

Query: 179 MVELANE-GMTMMVVTHEMGFARKVANRVIFMDEGKI 214
           + E+  E G T M +TH+M   R +A+ V  +  GKI
Sbjct: 188 IREIVVEMGATAMTITHDMTSVRAIADDVAMLHGGKI 224


Lambda     K      H
   0.320    0.135    0.383 

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: 167
Number of extensions: 14
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: 241
Length of database: 257
Length adjustment: 24
Effective length of query: 217
Effective length of database: 233
Effective search space:    50561
Effective search space used:    50561
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: 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