GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Alkalihalobacterium alkalinitrilicum DSM 22532

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  145 bits (366), Expect = 1e-39
 Identities = 101/324 (31%), Positives = 158/324 (48%), Gaps = 26/324 (8%)

Query: 5   NKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIV 64
           N KS ++    G I   L +++   I    +F S  N  NI  Q S  +IIALG   ++ 
Sbjct: 11  NYKSLIS--SYGTIIAGLGIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMA 68

Query: 65  TQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLING 124
            +  DLS G    L  V++A L  S              PI   +L+   +G V+G  NG
Sbjct: 69  VKEFDLSIGAMASLGGVLSALLAAS------------GTPIIFCLLVPIIVGFVVGFFNG 116

Query: 125 LIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLS 184
            I+    V  F+TTL    ++ G+            ++G  + F    +GF  LG  +L+
Sbjct: 117 AIVTKFKVLSFVTTLAMGTVIGGVTFW---------LTGGATVFENIPEGFKFLGQSKLA 167

Query: 185 YITFYALIAVAFVWVLW---NKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVF 241
           ++   ++I    V + W   ++T  G+ ++AIGGN +A++VSG+N+     + +AL G+ 
Sbjct: 168 FLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKASEVSGINIARYKNIAFALCGML 227

Query: 242 YAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINY 301
            AF G L A R+GSA    G  + L+A AA  +G      GV  ++G + G  I  ++  
Sbjct: 228 AAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVKNGVPNILGTLFGAAIIGIMAN 287

Query: 302 GLTYIGVNPYWQYIIKGAIIIFAV 325
           GLT + V  + Q II GAIII A+
Sbjct: 288 GLTILEVPSFIQNIITGAIIIIAL 311


Lambda     K      H
   0.327    0.143    0.415 

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: 308
Number of extensions: 19
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: 336
Length of database: 321
Length adjustment: 28
Effective length of query: 308
Effective length of database: 293
Effective search space:    90244
Effective search space used:    90244
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 (21.7 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