GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__Dino:3608829
          Length = 259

 Score =  206 bits (524), Expect = 4e-58
 Identities = 112/254 (44%), Positives = 161/254 (63%), Gaps = 12/254 (4%)

Query: 7   QPVSPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEH 66
           +P  P  +I+++ ++K YG   VLK +++  ++G+ + L G SGSGKST +RC N LE+ 
Sbjct: 3   EPTVP--VIEIRDLHKAYGALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDS 60

Query: 67  QQGRIVVDGVELT----------NDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPM 116
           Q+G ++  G  +T           D KQ+  IR  + MVFQ FNL+ H+TIL+N   AP+
Sbjct: 61  QRGDVLFCGEPVTWTGSGLDRRPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPV 120

Query: 117 WVRKMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEP 176
            V   P ++ E  A   L++V I ++   YP QLSGGQQQR AIAR L M+PK +LFDEP
Sbjct: 121 TVLGEPPKEVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEP 180

Query: 177 TSALDPEMVKEVLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDF 236
           TSALDPE+ +EV+  +  LA +G TML VTH+M  A  V++ V+F+ +G I E+  P+  
Sbjct: 181 TSALDPELEQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDIL 240

Query: 237 FDNPQNDRTKLFLS 250
           F  P++ R K FLS
Sbjct: 241 FGQPKSARLKQFLS 254


Lambda     K      H
   0.322    0.137    0.407 

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: 169
Number of extensions: 5
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: 254
Length of database: 259
Length adjustment: 24
Effective length of query: 230
Effective length of database: 235
Effective search space:    54050
Effective search space used:    54050
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: 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