GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Marinobacter adhaerens HP15

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__Marino:GFF3114
          Length = 423

 Score =  396 bits (1018), Expect = e-115
 Identities = 203/343 (59%), Positives = 255/343 (74%), Gaps = 5/343 (1%)

Query: 128 LSQAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGW 187
           L Q+ ++   ++  A+++    W+    VV+AL +PF     R  +D+  L+L YIML  
Sbjct: 76  LPQSNKEPMAENRRAKIES---WVLTGIVVLALFWPF--FVSRGAVDLATLVLIYIMLAL 130

Query: 188 GLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPV 247
           GLN+VVGLAGLLDLGYVAFYAVGAY++ALL+ Y G SFW+ LP+   LAA+ G++LGFPV
Sbjct: 131 GLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAALFGLVLGFPV 190

Query: 248 LRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAA 307
           LRLRGDY AIVTLGFGEIIRI+L NW   TGGPNGI GIP P+ FG+    R   EG  +
Sbjct: 191 LRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFGRRVKEEGNTS 250

Query: 308 FHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGI 367
           FHE FG+ +S  H++IFLY + LVLA+   L   R  ++P+GRAWEALRED+IA  SLG+
Sbjct: 251 FHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALREDEIAARSLGL 310

Query: 368 NRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVV 427
           +RT +KL+AF I A F GFAG+ FA++QGFISPESF F+ESAIILAIVVLGGMGSQIGVV
Sbjct: 311 SRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVLGGMGSQIGVV 370

Query: 428 VAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHR 470
           +AA  V  LPE  RE ++YRML FG  MVL+M+WRP+GL+  R
Sbjct: 371 LAAIAVTILPELAREFSEYRMLIFGAAMVLMMVWRPQGLMPMR 413


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: 579
Number of extensions: 23
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 505
Length of database: 423
Length adjustment: 33
Effective length of query: 472
Effective length of database: 390
Effective search space:   184080
Effective search space used:   184080
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: 51 (24.3 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