GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Shewanella loihica PV-4

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate 5208816 Shew_1318 polysaccharide biosynthesis protein CapD (RefSeq)

Query= curated2:A8GWP0
         (341 letters)



>FitnessBrowser__PV4:5208816
          Length = 332

 Score =  218 bits (554), Expect = 2e-61
 Identities = 139/335 (41%), Positives = 194/335 (57%), Gaps = 16/335 (4%)

Query: 1   MFVDKTLLITGGTGSFGNAVLSRFLKNDIIKDIKEIRIFSRDEKKQEDMRIALNNPKIKF 60
           MF +K++LITGGTGSFG       L+       K + I SRDE KQ +M+   N P +++
Sbjct: 1   MFNNKSILITGGTGSFGQKYTKTILER---YSPKRLIILSRDELKQYEMQQIYNAPCMRY 57

Query: 61  YIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATINKV 120
           ++GDVR+ + +  A KDVDYV HAAA+KQVP  E+ PME I TNI GAENV++AA  NKV
Sbjct: 58  FLGDVRDGDRMMQAFKDVDYVIHAAAIKQVPAAEYNPMECIKTNIHGAENVIKAAIANKV 117

Query: 121 AKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSVIP 180
            KVI LSTDKA  PIN  G +K   +KL +A   +    +T F   RYGNV+ SRGSV+P
Sbjct: 118 KKVIALSTDKAANPINLYGATKLASDKLFVAGNNIVGDGETRFSAVRYGNVVGSRGSVVP 177

Query: 181 LFINQIKQN-KDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVLA 239
            F   IK+  + L IT P MTRF ++L D VD VL  F     G+IFV K P+  I  LA
Sbjct: 178 FFQKLIKEGAQSLPITHPDMTRFWITLQDGVDFVLKNFSRMQGGEIFVPKIPSVRITDLA 237

Query: 240 KALQGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYY----RIPMDGRDLNYA 295
           +A    +        +G R GEK +E +  +++     +  +++     I   GR+ +Y+
Sbjct: 238 QA----YGPGLSHDIVGIRPGEKMHEIMCPADDSHHTIEFDDHFVITPSISFFGREHDYS 293

Query: 296 KYFVEGEKKIAL---LEDYTSHNTKRLNLEEVKEL 327
              + GEK   +    E ++ +N   L ++E+K L
Sbjct: 294 LNQL-GEKGSLVEQGFEYHSGNNPHFLTVDEIKLL 327


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: 301
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: 332
Length adjustment: 28
Effective length of query: 313
Effective length of database: 304
Effective search space:    95152
Effective search space used:    95152
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 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