GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Methanobacterium veterum MK4

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_048082461.1 EJ01_RS14630 polysaccharide biosynthesis protein

Query= SwissProt::Q9ZDJ5
         (341 letters)



>NCBI__GCF_000745485.1:WP_048082461.1
          Length = 364

 Score =  227 bits (579), Expect = 3e-64
 Identities = 124/291 (42%), Positives = 180/291 (61%), Gaps = 11/291 (3%)

Query: 2   FVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSKLKFY 61
           + DK +++TGGTGS G+ ++ + L+    +  K +R+   +E    ++   LN+ K++  
Sbjct: 5   YKDKVVLVTGGTGSIGSEIVKKLLE----HGPKVVRVLDNNETSLFELEHDLNSDKIRTL 60

Query: 62  IGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNKVT 121
           +GD+R+ + +  A  GVD VFHA ALK VP CEF P +A+ TNV+G +NVL+AA++  V+
Sbjct: 61  MGDIRDKERLMRAFEGVDIVFHAGALKHVPLCEFNPFDAVKTNVIGTQNVLNAALDQGVS 120

Query: 122 KVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVIPL 181
           KVIV+STDKAV PIN MG +K L E+L I+        ET+    R+GNV+ SRGSV+PL
Sbjct: 121 KVIVISTDKAVNPINVMGATKLLAERLTISANNYTGDKETVFSCVRFGNVLDSRGSVVPL 180

Query: 182 FIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTI----EV 237
           F  QIK+G  +TIT P MTRF+M +  +V L+L A E     +IF+ K PA  I    EV
Sbjct: 181 FKSQIKKGGPVTITSPDMTRFIMGIPQAVQLILKAGEISEGKEIFILKMPALNIVDLAEV 240

Query: 238 LAKALQEIFGSKN---AIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRI 285
           + +    ++G K     I+ IG R GEK YE L++ ++   A D G  Y I
Sbjct: 241 MIEEFAPLYGYKPEDIEIQIIGKRIGEKTYEELMTEDETVNAVDQGKLYII 291


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: 305
Number of extensions: 15
Number of successful extensions: 3
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: 364
Length adjustment: 29
Effective length of query: 312
Effective length of database: 335
Effective search space:   104520
Effective search space used:   104520
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