GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF1605 PS417_08165 UDP-glucose
           4-epimerase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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