GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Desulfovibrio vulgaris Hildenborough

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein

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



>lcl|MicrobesOnline__882:208249 DVU2743 high-affinity branched-chain
           amino acid ABC ransporter, permease protein
          Length = 306

 Score =  206 bits (523), Expect = 7e-58
 Identities = 112/310 (36%), Positives = 186/310 (60%), Gaps = 16/310 (5%)

Query: 8   FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67
           F+Q +FN +  GS YALIA+GYT+VYG++ +INFAHG+++M+G+Y+SF +  A +++G  
Sbjct: 4   FIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFV--ASILLGQI 61

Query: 68  TGWLLVAAGFVGAI------VIASAYGWSIERVAYRPVRN--SKRLIALISAIGMSIFLQ 119
            G+  ++     A+      V+ +  G ++ERVAYRP+R   + RL  +I+A+   I L+
Sbjct: 62  GGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIMLE 121

Query: 120 NYVSLTEGSRDVALPSLFNGQ-WVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYS 178
           N      G+   ALP + +   + +G     + S+T ++ ++ +  FL    L   +  +
Sbjct: 122 NGNLALLGASRKALPEMIDKVVYTIG-----TVSVTNLKLMVIVTAFLVFALLQFIVTRT 176

Query: 179 RMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMA 238
           R+G A RA A D     L+GI  D +I  TFV+G+  A +AG+L    Y +++PY+G M 
Sbjct: 177 RIGMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMV 236

Query: 239 GMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTG 298
           G KAF AAV+GGIG I GA IGG +L   E + +A   + ++D+ +F++L+ ++   PTG
Sbjct: 237 GWKAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTG 296

Query: 299 ILGRPEVEKV 308
           + G  +  K+
Sbjct: 297 LFGVAKTTKI 306


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: 235
Number of extensions: 7
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: 306
Length adjustment: 27
Effective length of query: 281
Effective length of database: 279
Effective search space:    78399
Effective search space used:    78399
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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