GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Paraburkholderia bryophila 376MFSha3.1

Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein

Query= SwissProt::P22729
         (425 letters)



>FitnessBrowser__Burk376:H281DRAFT_05513
          Length = 597

 Score =  143 bits (361), Expect = 1e-38
 Identities = 98/317 (30%), Positives = 159/317 (50%), Gaps = 25/317 (7%)

Query: 88  KQKLFLVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYA 147
           K   FL A+L+  + W +    G + IA       I  +G+N++VGLSG + LG   FYA
Sbjct: 15  KAPYFLCAILLAGLPWIWSGGFG-IHIAQSFCYTAIAVIGVNLLVGLSGQMSLGQAAFYA 73

Query: 148 IGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRI 207
           IGAY   L +   G      +     +AAA G ++G   LR RG YLA+ TL  G +V I
Sbjct: 74  IGAYASVLTSLKLGWPIAASVLFGVAVAAAVGTVVGVFALRTRGLYLAMTTLAVGFVVSI 133

Query: 208 LLLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLV 267
           L      +TGG  G+S +P+     ++F  T     W                  +LY+V
Sbjct: 134 LAQRWVGLTGGTMGLSGVPQ-----VDFGDTIHGEIW------------------YLYVV 170

Query: 268 ALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAG 327
              L+V+ + + + +    +GR   A R+ E    S+G+    ++   F +SAA AG +G
Sbjct: 171 GGTLLVVQI-LNDYVFDSRIGRCLLATRDSEAFAASVGIKVPIVRSAIFAVSAALAGLSG 229

Query: 328 TLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSM 387
            LFA + GFV  ++F+   S  +L   V+GG+G++   +    +L+   EL+   + Y +
Sbjct: 230 GLFAHQSGFVGSDAFSVTLSLSLLIAAVIGGLGARIGPLAGTAILMTIVELVAGLDRYGL 289

Query: 388 LMLGGLMVLMMIWRPQG 404
           ++ GG+M+L+++  PQG
Sbjct: 290 MVYGGIMLLVLLVFPQG 306


Lambda     K      H
   0.330    0.145    0.436 

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: 432
Number of extensions: 8
Number of successful extensions: 2
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: 425
Length of database: 597
Length adjustment: 34
Effective length of query: 391
Effective length of database: 563
Effective search space:   220133
Effective search space used:   220133
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: 52 (24.6 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