GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Methanospirillum lacunae Ki8-1

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_109969581.1 DK846_RS13945 SDR family NAD(P)-dependent oxidoreductase

Query= curated2:A8GWP0
         (341 letters)



>NCBI__GCF_003173355.1:WP_109969581.1
          Length = 343

 Score =  204 bits (518), Expect = 3e-57
 Identities = 129/342 (37%), Positives = 189/342 (55%), Gaps = 23/342 (6%)

Query: 5   KTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKFYIGD 64
           K +LITGG GS G+ ++   ++     D + IR+F  +E    D+   LN+ K++  IGD
Sbjct: 10  KRVLITGGVGSIGSVLVREIIQ----LDPEFIRVFDNNETALFDLEQDLNSQKLRPLIGD 65

Query: 65  VRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKVAKVI 124
           +R+   +  AM+ VD VFHAAALK VP CEF P +AI TN+LG +NVL A  I  V K+I
Sbjct: 66  IRDKARLVMAMEHVDIVFHAAALKHVPICEFNPFDAIKTNVLGTQNVLEAGLIQGVGKII 125

Query: 125 VLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIPLFIN 184
            +STDKAV P N MG +K L E+L I+        KT F   R+GNV+ SRGSVIP F+ 
Sbjct: 126 TVSTDKAVNPSNVMGATKLLAERLTISANSYRGHKKTAFSCVRFGNVLNSRGSVIPTFLK 185

Query: 185 QIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLAKALQG 244
           QI++   ++IT P M RF+M +  +  L+L A       +IF+ K P   I+ L + ++ 
Sbjct: 186 QIRKGGPISITHPDMRRFIMDIPSAAKLILIAGILAEGKEIFILKMPVIRIQDLGEVMKE 245

Query: 245 IFNSKN-------KIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRI-----PMDGRDL 292
           +F S         + + IG R GEK  E L++++E   A +  + Y I     P   + +
Sbjct: 246 MFASHYGYTPNDIETQIIGLRGGEKIDEVLMTTDETIAAYESDSMYLILPKERPYGNKTI 305

Query: 293 --NYAKYFVEGEKKIALLEDYTSHNTKRLNLEEVKELLLNLD 332
             N    F E  + I     Y+S +   L+ EE++ LL  L+
Sbjct: 306 KPNIPAGFRELSEGI-----YSSRDLPLLSKEEIRHLLAELE 342


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: 270
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: 343
Length adjustment: 29
Effective length of query: 312
Effective length of database: 314
Effective search space:    97968
Effective search space used:    97968
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.

Links

Downloads

Related tools

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