GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Dechlorosoma suillum PS

Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Dsui_2061 Dsui_2061 ABC-type branched-chain amino acid transport system, periplasmic component

Query= TCDB::Q8DQI1
         (386 letters)



>FitnessBrowser__PS:Dsui_2061
          Length = 384

 Score =  171 bits (434), Expect = 2e-47
 Identities = 117/342 (34%), Positives = 172/342 (50%), Gaps = 14/342 (4%)

Query: 27  GAVNTAGNSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGIDGKQIEVVD 86
           GA+  AG + +   IKIG     +G  A YG A + G QLA DEINA GG++G +I++V 
Sbjct: 12  GALAAAGLA-QAADIKIGVAAALTGGAAQYGVAIRNGFQLAADEINAKGGVNGNKIQLVV 70

Query: 87  KDNKSETAEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLT 146
           +D + +  E  +V   L+ Q KV  V GP  S +  AA   A  A   +   S T +G+T
Sbjct: 71  EDEQGKKEEGINVFKKLIFQDKVLMVFGPTLSNSMFAAGPVANGAKTVVFGTSVTANGIT 130

Query: 147 KGQDYLFIGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKG---IAKSFRESYKG 203
               Y+F  +  +S    +     ++    K+V +   N   + K    + K   E  K 
Sbjct: 131 DIGPYVFRNSVMESDVLPVTVATATKHYKLKQVAVIYGNDDAFTKSGYDVFKKVLEDQKL 190

Query: 204 EIVADETFVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGDG 263
            +   ET+V GD DF+A LTK+K  + DA++      EA  I+ QARG+GI  P +GG+G
Sbjct: 191 PVTTTETYVKGDVDFKAQLTKIKASNPDAVICSCLAEEAANIMLQARGLGIKVPFIGGNG 250

Query: 264 FNGEEFVQQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYNEEPSTFAALAYDSV 323
           FN  +  +   ++ A    F+    +    +   KAF+ AY  KYN EP+ FAA A+D++
Sbjct: 251 FNSPKLFE--ISKLAGEGTFVGSPWSNTNPAPANKAFVAAYVKKYNAEPNQFAAQAFDAL 308

Query: 324 HLVANAAKGAKNSGEI-------KNNLAKTKDFEGVTGQTSF 358
           H+ A A +  K SG+I       KN L K     G TG   F
Sbjct: 309 HVAAAALQEVKLSGDIAADREALKNALPKA-TINGATGPFKF 349


Lambda     K      H
   0.310    0.126    0.337 

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: 333
Number of extensions: 17
Number of successful extensions: 3
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: 386
Length of database: 384
Length adjustment: 30
Effective length of query: 356
Effective length of database: 354
Effective search space:   126024
Effective search space used:   126024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 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