GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Shewanella oneidensis MR-1

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 202283 SO3173 UDP-galactose 4-epimerase, putative (NCBI ptt file)

Query= curated2:Q56623
         (328 letters)



>FitnessBrowser__MR1:202283
          Length = 309

 Score =  295 bits (754), Expect = 1e-84
 Identities = 156/308 (50%), Positives = 210/308 (68%), Gaps = 7/308 (2%)

Query: 10  KSILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLK 69
           +SILLTG+TGFVG  +++ L   +    ++      +      F  G++ A+TD+   L 
Sbjct: 4   QSILLTGATGFVGQQILRQLPQDTRVFGRTKPARDCH------FFAGELTANTDYRSALS 57

Query: 70  NTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGE 129
              VV+HCAARAHVM++       LY+EVNT  T+ LA+QA  +GVKRFIFIS+IKVNGE
Sbjct: 58  GVDVVIHCAARAHVMNETANNAAQLYQEVNTLVTLALAEQAAAAGVKRFIFISTIKVNGE 117

Query: 130 GTLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFA 189
            T+ G  F+  D   P D YG SK++AE  L  +A+ + +EVVIIRP +VYGP VKANFA
Sbjct: 118 ATIAGQLFRASDARQPLDHYGESKAKAEIGLFDIARKTEIEVVIIRPPLVYGPNVKANFA 177

Query: 190 SLMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAE 249
           +++ L  K +PLPFG+I  NKRS+V+++NLVDLIVTCI+HP AANQ+FLVSD  DVST E
Sbjct: 178 TMLNLAKKNLPLPFGAI-HNKRSMVALDNLVDLIVTCIEHPNAANQIFLVSDDQDVSTTE 236

Query: 250 MVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQ 309
           +++ +  A  K    LPVP+    L GK+ G   I+DRL G LQVDI+HTK TL W+PP 
Sbjct: 237 LLKLMTGAAGKKPRLLPVPMAWLILAGKVTGNQAIIDRLCGNLQVDITHTKNTLSWQPPI 296

Query: 310 TLQEGFKQ 317
           T++EG ++
Sbjct: 297 TVEEGVRR 304


Lambda     K      H
   0.318    0.134    0.388 

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: 289
Number of extensions: 11
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: 328
Length of database: 309
Length adjustment: 27
Effective length of query: 301
Effective length of database: 282
Effective search space:    84882
Effective search space used:    84882
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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