GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Dinoroseobacter shibae DFL-12

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 3608113 Dshi_1518 inner-membrane translocator (RefSeq)

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>lcl|FitnessBrowser__Dino:3608113 Dshi_1518 inner-membrane
           translocator (RefSeq)
          Length = 336

 Score =  125 bits (313), Expect = 2e-33
 Identities = 95/315 (30%), Positives = 156/315 (49%), Gaps = 40/315 (12%)

Query: 19  GSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTGWL---LVAA 75
           GS  AL A+G T++YGI+   NFAHG+    G+  + +   A   +GI  G L   L+A 
Sbjct: 22  GSQLALGALGVTLIYGILRFSNFAHGDTMAFGTMATILFTWAFQSIGISLGPLPTALLAL 81

Query: 76  GFVGAIVIASAYGWSIERVAYRPVRNSKRL--IALISAIGMSIFLQNYVSLTEGSRDVAL 133
            F   I++  A     +R+ Y+  R  K +  I +I+++G+       V    G  D   
Sbjct: 82  PF--GILVTGALLVGTDRLVYKFYRQQKAVPVIFVIASLGVMFVTNALVRFIIGPDDQRF 139

Query: 134 PSLFNGQWVVGHSENF--------SASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACR 185
               +G+  +  +  F          ++ T Q +  +   + +  L  F+  +R G++ R
Sbjct: 140 A---DGERFIISAREFRNLTGLDEGLALRTTQGLTVVTAVIVVALLFWFLNRTRTGKSMR 196

Query: 186 ACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTA 245
           A +++  +A L GIN +RV+ +T++I AA+A VAG L G       P+  F   +  F A
Sbjct: 197 AFSDNEDLALLSGINPERVVMVTWLIVAALATVAGTLYG-LDKSFKPFTYFQLLLPIFAA 255

Query: 246 AVLGGIGSIPGAMIGGLILGIAE-ALSSAY--------------------LSTEYKDVVS 284
           A++GG+GS  GA+ GG ++  +E  ++ A+                    LST+YK  VS
Sbjct: 256 AIVGGLGSPLGAIAGGFVIAFSEVTITYAFKKVLEYLLPEALEPDGLVQLLSTDYKFAVS 315

Query: 285 FALLILVLLVMPTGI 299
           FA+LI+VLL  PTG+
Sbjct: 316 FAILIIVLLFKPTGL 330


Lambda     K      H
   0.328    0.141    0.410 

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: 244
Number of extensions: 15
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: 308
Length of database: 336
Length adjustment: 28
Effective length of query: 280
Effective length of database: 308
Effective search space:    86240
Effective search space used:    86240
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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