GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:206139
          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:

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