GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pseudomonas simiae WCS417

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate GFF1605 PS417_08165 UDP-glucose 4-epimerase

Query= SwissProt::Q9ZDJ5
         (341 letters)



>FitnessBrowser__WCS417:GFF1605
          Length = 344

 Score =  436 bits (1121), Expect = e-127
 Identities = 219/336 (65%), Positives = 274/336 (81%), Gaps = 5/336 (1%)

Query: 1   MFVDKTLMITGGTGSFGNAVLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSKLKF 60
           MF  KTL+ITGGTGSFGNAVL RFL S I     EIRIFSRDEKKQ+DMR    ++KLKF
Sbjct: 1   MFSGKTLLITGGTGSFGNAVLKRFLDSGIA----EIRIFSRDEKKQDDMRKRYADTKLKF 56

Query: 61  YIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAINNKV 120
           YIGDVR+YQS+ +A  GVDY+FHAAALKQVP+CEF+PMEA+ TNV+G ENVL AAI N V
Sbjct: 57  YIGDVRDYQSVLNATRGVDYIFHAAALKQVPSCEFHPMEAVKTNVIGTENVLEAAIQNSV 116

Query: 121 TKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRGSVIP 180
            +V+ LSTDKAVYPINAMG+SKA+MEK+ IAK+R     +T++C TRYGNVMASRGSVIP
Sbjct: 117 KRVVCLSTDKAVYPINAMGISKAMMEKVMIAKSRNVDDAKTVICGTRYGNVMASRGSVIP 176

Query: 181 LFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIEVLAK 240
           LFI QI+ G  LT+T+PSMTRF+M+L D+VDLVLYAFEHGR GD+FVQK+PA+T+E LAK
Sbjct: 177 LFIEQIRAGNALTLTDPSMTRFMMTLADAVDLVLYAFEHGRNGDLFVQKAPAATVETLAK 236

Query: 241 ALQEIFGS-KNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRIPMDGRDLNYAKYFV 299
           AL  + G  ++ I+ IGTRHGEK +E+L+S E+MA A+D G YYRIP D RDLNY+K+  
Sbjct: 237 ALTAMVGKPEHPIQVIGTRHGEKLFEALLSREEMACAEDKGDYYRIPPDLRDLNYSKFVE 296

Query: 300 TGEKKVALLDDYTSHNTKRLNLKEVKELLLTLDYVQ 335
            GE+K++  +DY SHNT+RL++  ++ LLL L++++
Sbjct: 297 QGEEKISRTEDYNSHNTERLDVAGMQRLLLKLEFMK 332


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: 394
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: 341
Length of database: 344
Length adjustment: 29
Effective length of query: 312
Effective length of database: 315
Effective search space:    98280
Effective search space used:    98280
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