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 8500844 DvMF_1582 inner-membrane translocator (RefSeq)

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__Miya:8500844
          Length = 313

 Score =  131 bits (329), Expect = 4e-35
 Identities = 101/324 (31%), Positives = 161/324 (49%), Gaps = 39/324 (12%)

Query: 151 LGPIAVVVALA-FPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAV 209
           L P+ V+  LA  P   L +  ++ I IL + + + G   N++ G  G +  G+ AF+ +
Sbjct: 5   LVPLVVLAMLAGLPLLGL-NSYVMHILILSIMWTLAGMAWNLLGGYCGQVSFGHAAFFGM 63

Query: 210 GAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRII 269
           GAYS  L+  + G S W    ++  L A+  + +G  VLRLRG YF + TL  GE++RI 
Sbjct: 64  GAYSAGLIHLHLGLSPWWGFLVSLPLVALVALAMGSVVLRLRGPYFVLATLAIGEVLRIT 123

Query: 270 LINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLI 329
             N   FT G  GI              TRT  E T                    YY+I
Sbjct: 124 CENLTDFTKGTLGIM------------ITRTWVEKTQ------------------YYYII 153

Query: 330 LVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGS 389
           L LAL+  +    +     G  + A+RED  A  S+GI+ T  K  A  ++AM  G AG+
Sbjct: 154 LGLALLGFVVCRAIVHSRWGYYFVAIREDQDAAESMGIDTTRYKTIALTVSAMLTGLAGA 213

Query: 390 FFATRQGFISP-ESFTFIE-SAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFREL---- 443
           F+    G+I P   F+  E S +I+ +V++GG+ ++ G  + A +++ L E  R L    
Sbjct: 214 FYTNYMGYIDPGVVFSLGEISILIIMVVMVGGVATEWGPALGAGIMVILAEYIRSLPLIG 273

Query: 444 ADYRMLAFGMGMVLIMLWRPRGLL 467
             Y+ + FG+ +++I+++ P GL+
Sbjct: 274 VAYQTM-FGVLLIVIIIYLPNGLV 296


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: 435
Number of extensions: 28
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: 505
Length of database: 313
Length adjustment: 31
Effective length of query: 474
Effective length of database: 282
Effective search space:   133668
Effective search space used:   133668
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