GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Azospirillum brasilense Sp245

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate AZOBR_RS32415 AZOBR_RS32415 branched-chain amino acid ABC transporter permease

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



>FitnessBrowser__azobra:AZOBR_RS32415
          Length = 305

 Score =  195 bits (495), Expect = 1e-54
 Identities = 106/306 (34%), Positives = 184/306 (60%), Gaps = 21/306 (6%)

Query: 6   LYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMG 65
           ++FLQQ+ NG+++G  YAL+AIG+T+++G++ ++NFAHGEVY IG++V  M+I A+    
Sbjct: 5   VFFLQQVINGLSIGCVYALMAIGFTLIFGVLNVVNFAHGEVYTIGAFVGLMVITAMAPPL 64

Query: 66  IDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRN----------SKRLIALISAIGMS 115
           +    L++A G V  +         +ER+A+RP R           + R   L+S++ +S
Sbjct: 65  LAVVPLVLAVGAVSGV--------GLERIAFRPFRRFTDEASQKSRAMREATLLSSLAVS 116

Query: 116 IFLQNYVSLTEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFI 175
           I  +  +    G     +PS +  Q  V       AS +    VI+  + + + AL   +
Sbjct: 117 IMTREIMMHIFGGDMQGIPSGYLLQQPVAIGPIMVASGSL---VIFATSAVMLGALQFLL 173

Query: 176 RYSRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIG 235
             ++ G   RA + +   A  +GINTDR I  TF +G+ + A AG+L+G + G I+P++G
Sbjct: 174 YRTQTGLGIRAVSNNQLGARYVGINTDRTIVTTFAVGSMLGATAGILVGLYDGAISPHMG 233

Query: 236 FMAGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVM 295
           F  G+KAF A V+GG+ SIPGA+   L+LG++E++++ +LS+ +KD+++++LL++ L+  
Sbjct: 234 FAPGVKAFVAMVMGGLSSIPGAVACALLLGVSESIATEFLSSGWKDLITYSLLVITLVFF 293

Query: 296 PTGILG 301
           P G+ G
Sbjct: 294 PQGLFG 299


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: 223
Number of extensions: 10
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: 305
Length adjustment: 27
Effective length of query: 281
Effective length of database: 278
Effective search space:    78118
Effective search space used:    78118
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