GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Desulfovibrio vulgaris Miyazaki F

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 8502039 DvMF_2752 inner-membrane translocator (RefSeq)

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__Miya:8502039
          Length = 330

 Score =  222 bits (566), Expect = 1e-62
 Identities = 138/345 (40%), Positives = 188/345 (54%), Gaps = 30/345 (8%)

Query: 154 IAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYS 213
           IAVVVA+      L D    D+ + +  Y +L   LNI++G AGL  +G+ AFYAVGAY 
Sbjct: 12  IAVVVAV---LPLLLDPYWTDVFVSIGLYSVLALSLNIILGQAGLFHMGHAAFYAVGAYV 68

Query: 214 YALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILI-N 272
            A+    +G      +P AG  AA+  +++  P++ LRGDY  IVT+G  EI+RI LI N
Sbjct: 69  TAIANTMWGVPVLWAMPFAGLAAALFAMVVARPIIHLRGDYLLIVTIGIVEIVRIALINN 128

Query: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVL 332
            +  TGG NGI GI RP  FG                         + + +  YYL+   
Sbjct: 129 VFGLTGGANGIFGISRPMLFGF-----------------------KIAKPVHFYYLVWAY 165

Query: 333 ALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFA 392
                L   R+     GRA   ++EDD A    G+N  + KL AF + A + G  G+ +A
Sbjct: 166 VACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFWAGMTGTIYA 225

Query: 393 TRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFG 452
            +   ISPESF+F ES ++ AIV+LGG GS  GV++ AFL+IGLPE FRE A  RMLAFG
Sbjct: 226 AKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFREFASARMLAFG 284

Query: 453 MGMVLIMLWRPRGLLAHRDPTILLHGRPK--GGAGGPAAGSAAAG 495
           + MV++M++RP+G+L        L  R +   G GG AA  A  G
Sbjct: 285 LAMVVMMIFRPQGMLPPMPRFYKLPERIRCITGKGGDAAAQAGGG 329



 Score = 25.4 bits (54), Expect = 0.003
 Identities = 30/106 (28%), Positives = 43/106 (40%), Gaps = 20/106 (18%)

Query: 32  TIPLVGLRTVDRPTGLGLETRWNEVAAAVGL---------VFLGRLGLCLIREGH----A 78
           T    G+  V     L L+  W +V  ++GL         + LG+ G  L   GH    A
Sbjct: 6   TTSYAGIAVVVAVLPLLLDPYWTDVFVSIGLYSVLALSLNIILGQAG--LFHMGHAAFYA 63

Query: 79  VTVLVLAAAATAAGFFI--AMPTEALRVILIAGGAVIAIRAVLAIR 122
           V   V A A T  G  +  AMP   L   L    A++  R ++ +R
Sbjct: 64  VGAYVTAIANTMWGVPVLWAMPFAGLAAALF---AMVVARPIIHLR 106


Lambda     K      H
   0.329    0.144    0.438 

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: 444
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 505
Length of database: 330
Length adjustment: 31
Effective length of query: 474
Effective length of database: 299
Effective search space:   141726
Effective search space used:   141726
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: 50 (23.9 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