GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Dechlorosoma suillum PS

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate Dsui_0083 Dsui_0083 UDP-N-acetylglucosamine 4,6-dehydratase

Query= SwissProt::Q9ZDJ5
         (341 letters)



>FitnessBrowser__PS:Dsui_0083
          Length = 332

 Score =  205 bits (522), Expect = 1e-57
 Identities = 125/327 (38%), Positives = 193/327 (59%), Gaps = 10/327 (3%)

Query: 1   MFVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALN-NSKLK 59
           M  + +++ITGGTGSFGN  +   L      + K+I IFSRDE KQ +M      + +++
Sbjct: 1   MLTNTSILITGGTGSFGNTFVPMTLAKF---NPKKIVIFSRDEMKQWEMAKKFGGDERVR 57

Query: 60  FYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNK 119
           F+IGDVR+ + +  A+ G+DYV HAAA K VPT E+ P E + TN+ GA N++ A I+  
Sbjct: 58  FFIGDVRDRERLYRALDGIDYVVHAAATKIVPTAEYNPFECVKTNINGAMNLIDACIDKG 117

Query: 120 VTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVI 179
           V +V+ LSTDKA  P+N  G +K   +KL +A        +T   V RYGNVM SRGSVI
Sbjct: 118 VKRVVALSTDKASSPVNLYGATKLASDKLFVAGNSYAGGHDTRFAVVRYGNVMGSRGSVI 177

Query: 180 PLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVLA 239
           P F+  IK    L IT+  MTRF++SL   V+LV +AF     G+I+V+K P+  +  LA
Sbjct: 178 PFFM-SIKDKGVLPITDERMTRFMISLEQGVELVWHAFGDMEGGEIYVKKIPSMKVTDLA 236

Query: 240 KALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAKYFV 299
           +A+        ++ ++G R GEK +E ++S ED   + +   +++I     + + +   +
Sbjct: 237 RAI----APNASLEYVGIRPGEKLHEQMISEEDALYSYEYPEHFKILPAIHNWHLSPGRI 292

Query: 300 TGEKKVALLDDYTS-HNTKRLNLKEVK 325
              KKV     YTS +N++ + ++E++
Sbjct: 293 KDGKKVPEGFSYTSDNNSEWMGIEELQ 319


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: 299
Number of extensions: 21
Number of successful extensions: 5
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