GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5504 in Dechlorosoma suillum PS

Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Dsui_2067 Dsui_2067 ABC-type metal ion transport system, permease component

Query= TCDB::Q9HT69
         (225 letters)



>FitnessBrowser__PS:Dsui_2067
          Length = 232

 Score =  187 bits (475), Expect = 1e-52
 Identities = 100/204 (49%), Positives = 143/204 (70%), Gaps = 1/204 (0%)

Query: 16  EIWLASVDTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSL-VVNILRSL 74
           EI  A+ +T  M+   L   V++G  LG+L+FLT P Q+  +   + L++   +N+ RS 
Sbjct: 22  EIGKAAGETGLMMLICLTAAVIVGGALGILVFLTSPGQVLGRYRRFNLVANGFINVFRSF 81

Query: 75  PFIILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKGIIEATQAM 134
           PFIILL+ + P T  I GTS+G   A  PL + A  +FAR++E  LR+V +G+IEA +AM
Sbjct: 82  PFIILLVAVSPFTRHIVGTSIGPLAASVPLSLAAIFYFARIIEQTLRDVPRGVIEAAEAM 141

Query: 135 GASTRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIRFGYQRFQT 194
           GAS  QI+   LL EAR G+I A+T+TA++ +SY+A+AGVVG GG+GDLAIR+GY RFQT
Sbjct: 142 GASPLQIVTQVLLVEARSGLILAVTITAVSFLSYSAVAGVVGGGGIGDLAIRYGYYRFQT 201

Query: 195 DVMVVTVVMLLILVQILQTVGDKL 218
           DVM++T+V+L++LVQ +Q  G  L
Sbjct: 202 DVMLITIVLLVVLVQGIQFFGQWL 225


Lambda     K      H
   0.329    0.143    0.419 

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: 123
Number of extensions: 3
Number of successful extensions: 1
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: 225
Length of database: 232
Length adjustment: 23
Effective length of query: 202
Effective length of database: 209
Effective search space:    42218
Effective search space used:    42218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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