GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:208249
          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 (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