GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Halococcus hamelinensis 100A6

Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_007690593.1 C447_RS02500 GDP-mannose 4,6-dehydratase

Query= curated2:Q57664
         (305 letters)



>NCBI__GCF_000336675.1:WP_007690593.1
          Length = 326

 Score =  221 bits (563), Expect = 2e-62
 Identities = 124/320 (38%), Positives = 181/320 (56%), Gaps = 23/320 (7%)

Query: 1   MILVTGGAGFIGSHIVDKLIENNYDVIILDNLT----TGNKNNINPKA----------EF 46
           MILVTGGAGFIG H+ +  +   +DV+ LDNL      G K      A          EF
Sbjct: 1   MILVTGGAGFIGGHLAETFVREGHDVVALDNLEPFYDVGIKRRTIEAARTAAEDGGSYEF 60

Query: 47  VNADIRDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYD 106
           V  D+RD +    +   D E V HQAAQ  VR SVENP    DINV GT+N+L+  R+  
Sbjct: 61  VEGDVRDAETVHDL-VADAEYVFHQAAQAGVRTSVENPRKVDDINVEGTLNVLDAARESG 119

Query: 107 IDKIVFASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILR 166
           ++++VFASS  +VYG+P  LP  E+ P  P+SPYG+SK   E Y+++Y  LY I    LR
Sbjct: 120 VERVVFASSS-SVYGKPVSLPYQEDQPTTPVSPYGVSKLAAENYVRVYGDLYDIPTVALR 178

Query: 167 YSNVYGERQDPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNW- 225
           Y  VYG R  P      IS F+ +   ++ P+++GDG+QTRDF YV D+ +AN   L+  
Sbjct: 179 YFTVYGPRMRPN---MAISNFVSRCTNDEPPVVYGDGSQTRDFTYVADIVRANAKLLDTD 235

Query: 226 --KNEIVNIGTGKETSVNELFDIIKHEIGFRGEAIYDKPREGEVYRIYLDIKKA-ESLGW 282
               E +NIG+    S+  L   ++  I    +  Y + + G+    + D+ KA E +G+
Sbjct: 236 AADGETMNIGSTDTVSIETLATTVRDAIAPELDIEYGERQAGDAEHTHADVSKAGELIGY 295

Query: 283 KPEIDLKEGIKRVVNWMKNN 302
           +P  D++ G++R ++W ++N
Sbjct: 296 EPTEDIRSGVERFIDWYQDN 315


Lambda     K      H
   0.317    0.140    0.405 

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: 320
Number of extensions: 16
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: 305
Length of database: 326
Length adjustment: 27
Effective length of query: 278
Effective length of database: 299
Effective search space:    83122
Effective search space used:    83122
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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