GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease

Query= uniprot:D8IZC8
         (344 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  185 bits (469), Expect = 2e-51
 Identities = 104/289 (35%), Positives = 165/289 (57%), Gaps = 1/289 (0%)

Query: 47  GLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVL 106
           G+ +  S    S+FAS +N +NI RQ++  +++A G T V+     DLS+G++ ++  VL
Sbjct: 27  GIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVL 86

Query: 107 GMQVSLGAAPG-WAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLAD 165
              ++    P  + + + I  G V+G  NGA+V    + +FV TL   T   G  + L  
Sbjct: 87  SALLAASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLTG 146

Query: 166 GTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAA 225
           G TV  N    F+++G      +P L  +   +V++ W I+ +T LG  +YAIGGN +A+
Sbjct: 147 GATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKAS 206

Query: 226 RLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLM 285
            ++GI +       +++ G+ +   GA+ ASRL  A+   G G+ L+A AAV LG T + 
Sbjct: 207 EVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVK 266

Query: 286 GGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDK 334
            GV +I GT+ GA IIG+M NGLTIL + SF Q +  GA+I++A+I  K
Sbjct: 267 NGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALISQK 315


Lambda     K      H
   0.324    0.138    0.417 

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: 312
Number of extensions: 22
Number of successful extensions: 2
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: 344
Length of database: 321
Length adjustment: 28
Effective length of query: 316
Effective length of database: 293
Effective search space:    92588
Effective search space used:    92588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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