GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Methanobacterium veterum MK4

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_048082709.1 EJ01_RS16035 polysaccharide biosynthesis protein

Query= curated2:A8GWP0
         (341 letters)



>NCBI__GCF_000745485.1:WP_048082709.1
          Length = 331

 Score =  219 bits (559), Expect = 6e-62
 Identities = 132/334 (39%), Positives = 190/334 (56%), Gaps = 26/334 (7%)

Query: 5   KTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKFYIGD 64
           KT+L+TGG GS G+ ++   L+     D K IR+   +E    ++   LN+ KI+  IGD
Sbjct: 13  KTILVTGGAGSIGSEIVRNLLE----LDPKAIRVLDNNETGLFELEQELNSDKIRTLIGD 68

Query: 65  VRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKVAKVI 124
           +R+   +  A + VD +FHAAALK VP CE+ P +A+ TN++G +NVL AA    V K I
Sbjct: 69  IRDKERLMRAFEGVDIIFHAAALKHVPLCEYNPFDAVKTNVIGTQNVLDAALDQNVGKAI 128

Query: 125 VLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIPLFIN 184
           V+STDK V P+N MG +K L E+L I+        KTVF   R+GNV+ SRGSV+P+F N
Sbjct: 129 VISTDKTVNPVNVMGATKLLAERLTISANYYKGDKKTVFSCVRFGNVLDSRGSVVPIFKN 188

Query: 185 QIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLAKA--- 241
           QIK    +TIT+  MTRF+M +  +V L++ A       +IF+ K PA  I  LAKA   
Sbjct: 189 QIKNGGPVTITDYEMTRFVMGIPQAVGLIIKAGVIAEGNEIFILKMPAVNIIDLAKAMID 248

Query: 242 ----LQGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRIPMDGRDLNYAKY 297
               + G    + KI  IG R GEK +E L++ +E+             MD  DL    Y
Sbjct: 249 ELSPIYGYKPEEIKIEIIGKRLGEKLFEELMNEDELDYV----------MDNGDL----Y 294

Query: 298 FVEGEKKIALLE-DYTSHNTKRLNLEEVKELLLN 330
            +  E+ +   E  Y S+N  +LN +++K++L N
Sbjct: 295 ILNSERVLKKPEIHYNSNNALKLNKKQIKDVLKN 328


Lambda     K      H
   0.319    0.135    0.373 

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: 13
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: 341
Length of database: 331
Length adjustment: 28
Effective length of query: 313
Effective length of database: 303
Effective search space:    94839
Effective search space used:    94839
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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