GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Caldicellulosiruptor hydrothermalis 108

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_013403236.1 CALHY_RS06830 branched-chain amino acid ABC transporter permease

Query= uniprot:G8ALI9
         (505 letters)



>NCBI__GCF_000166355.1:WP_013403236.1
          Length = 312

 Score =  182 bits (463), Expect = 1e-50
 Identities = 115/323 (35%), Positives = 180/323 (55%), Gaps = 41/323 (12%)

Query: 155 AVVVALAFPFTPLADRQLLDIGI-----LLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAV 209
           A ++ L    T L    ++D  I     L++  I+L   LN++ G+ G   LG+  F A+
Sbjct: 10  AFIIVLYLTITLLMKIGIIDDYIKLNLFLIMLNIILAVSLNLINGITGQFSLGHAGFMAI 69

Query: 210 GAYSYALLAHYFG-FSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRI 268
           GAY+ A+L        F++ + + G  A + G+++G PVLRLRGDY AI TLGFGEIIR+
Sbjct: 70  GAYTTAVLTTLEKPVPFYLTVLIGGLFAMICGLIIGLPVLRLRGDYLAIATLGFGEIIRV 129

Query: 269 ILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYL 328
           I+ N   + GG +GIS IP+                        G++++        Y++
Sbjct: 130 IIQN-IDYLGGASGISDIPQ------------------------GIDWTG-------YFV 157

Query: 329 ILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAG 388
           I VL++VV L    +     GRA  A+RED+IA  ++GIN T  K+ AF I A F G AG
Sbjct: 158 ITVLSVVVIL---NIINSSFGRAMIAIREDEIAAEAMGINTTLYKVLAFMIGAFFAGVAG 214

Query: 389 SFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRM 448
           S ++   GFI P+ F F +S  IL IVVLGG+GS  G +++A ++  +    ++    RM
Sbjct: 215 SIYSGSFGFIQPDMFNFFKSIDILVIVVLGGLGSISGSIISAIVLTIISALLQDYPAVRM 274

Query: 449 LAFGMGMVLIMLWRPRGLLAHRD 471
           + + + +++IML+RP+GL+  ++
Sbjct: 275 VLYSLILIIIMLFRPQGLMGTKE 297


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: 394
Number of extensions: 26
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: 312
Length adjustment: 31
Effective length of query: 474
Effective length of database: 281
Effective search space:   133194
Effective search space used:   133194
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 24 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