GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08240 in Desulfovibrio vulgaris Hildenborough

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 206139 DVU0714 branched-chain amino acid ABC transporter, permease protein

Query= uniprot:G8ALI9
         (505 letters)



>lcl|MicrobesOnline__882:206139 DVU0714 branched-chain amino acid
           ABC transporter, permease protein
          Length = 317

 Score =  219 bits (559), Expect = 8e-62
 Identities = 127/315 (40%), Positives = 184/315 (58%), Gaps = 28/315 (8%)

Query: 154 IAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYS 213
           +AV++A+   F    D    D+ + +  Y +L   LN+++G AGL  +G+ AFYAVGAY+
Sbjct: 11  LAVLIAVLPLFL---DPYWTDVCVSIGLYAVLALSLNLILGQAGLFHMGHAAFYAVGAYT 67

Query: 214 YALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILI-N 272
            A+L   +       +P+AG LAA+  +++  P++ LRGDY  IVT+G  EI+RI LI N
Sbjct: 68  AAILNTVYHVPVLWTMPVAGLLAALFALVVARPIIHLRGDYLLIVTIGIVEIVRIALINN 127

Query: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVL 332
            +  TGG NGI GI RP  FG                         + + I  YYLI   
Sbjct: 128 VFGITGGANGIFGISRPMLFGY-----------------------KISKPIQFYYLIWTW 164

Query: 333 ALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFA 392
             +  L   R+     GRA   ++EDD+A    G++    KLAAF + A++ G  G+F+A
Sbjct: 165 VAISILLFRRLECSRFGRALNYIKEDDVAAEGSGVDTAYYKLAAFVLGALWAGMTGTFYA 224

Query: 393 TRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFG 452
            +   ISPESF+F ES ++ AIV+LGG GS  GV++ AFL+IGLPE FR+ A  RML FG
Sbjct: 225 AKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPELFRDFASARMLIFG 283

Query: 453 MGMVLIMLWRPRGLL 467
           + MV++M++RP+G+L
Sbjct: 284 LAMVVMMIFRPQGML 298



 Score = 24.3 bits (51), Expect = 0.007
 Identities = 27/118 (22%), Positives = 46/118 (38%), Gaps = 26/118 (22%)

Query: 17  ILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGL---------VFLGR 67
           I ++A+      L+  +PL             L+  W +V  ++GL         + LG+
Sbjct: 2   ISRKASYAGLAVLIAVLPLF------------LDPYWTDVCVSIGLYAVLALSLNLILGQ 49

Query: 68  LGLCLIREGHAVTVLVLAAAATAAGFFIAMP---TEALRVILIAGGAVIAIRAVLAIR 122
            G  L   GHA    V A  A        +P   T  +  +L A  A++  R ++ +R
Sbjct: 50  AG--LFHMGHAAFYAVGAYTAAILNTVYHVPVLWTMPVAGLLAALFALVVARPIIHLR 105


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: 397
Number of extensions: 23
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: 317
Length adjustment: 31
Effective length of query: 474
Effective length of database: 286
Effective search space:   135564
Effective search space used:   135564
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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