GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Dechlorosoma suillum PS

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component

Query= TCDB::Q8DQH9
         (318 letters)



>FitnessBrowser__PS:Dsui_2059
          Length = 287

 Score =  167 bits (423), Expect = 3e-46
 Identities = 96/280 (34%), Positives = 159/280 (56%), Gaps = 8/280 (2%)

Query: 35  YVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGAFFGAM 94
           Y  ++  +G++ +LA+ + L +   G  SL +A FM +GAY +A++        +F   +
Sbjct: 11  YSTLVFSVGVHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTLHLEW--SFGSVL 67

Query: 95  LVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILGIPNF 154
           L G +    VAL++G P LRL G YLA+ATL   E++RI ++N   +T G  G+ GIP  
Sbjct: 68  LAGGIAPTLVALIIGAPVLRLSGVYLAMATLAFGEVVRITVLNL-EITGGPEGLNGIPLA 126

Query: 155 TTWQMVYFFVVITTIATLNFLRSPIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAIT 214
           T    +   + +         RS +GR+  +++EDE+AA  +G+N  + K++AF  GA  
Sbjct: 127 TEGWHIALILAVAVYGLARLRRSKVGRAFEAIKEDEVAARLMGINVDRYKLLAFSLGAFI 186

Query: 215 ASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDV 274
           A +AG+L A F   + P++Y F N++++L + V GG  S+ G ++ + +L +L  LL+ +
Sbjct: 187 AGVAGALNAHFTFFISPREYGFENAVDILTMAVLGGTSSLIGPMLGSSILTLLPELLRSL 246

Query: 275 ASVRMIIYALALVLVMIFRPGGLLGTWELSLSR-FFKKSK 313
              R ++    LVLV++F P GL   WE    R FFK+ K
Sbjct: 247 QDFRSLVNGAVLVLVVLFLPKGL---WESRRIRAFFKRLK 283


Lambda     K      H
   0.327    0.143    0.403 

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: 196
Number of extensions: 8
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: 318
Length of database: 287
Length adjustment: 27
Effective length of query: 291
Effective length of database: 260
Effective search space:    75660
Effective search space used:    75660
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 (21.6 bits)
S2: 48 (23.1 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