GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysDH in Sinorhizobium meliloti 1021

Align lysine 6-dehydrogenase (EC 1.4.1.18) (characterized)
to candidate SMc02503 SMc02503 hypothetical protein

Query= BRENDA::Q3S559
         (368 letters)



>lcl|FitnessBrowser__Smeli:SMc02503 SMc02503 hypothetical protein
          Length = 367

 Score =  372 bits (954), Expect = e-107
 Identities = 190/354 (53%), Positives = 238/354 (67%), Gaps = 3/354 (0%)

Query: 8   ITVLGAGKIGFAIALLLQRTGDYAVCVADQDPSRLDAVA---ALGCQTAQIDNDAALEAA 64
           I V+GAGKIG  IA +L  +GDY VCVAD+   +L  V    A+      I +  AL A 
Sbjct: 4   IVVIGAGKIGSTIARMLAHSGDYRVCVADRSAEQLQQVEKHDAVSTAVVDIADRKALVAL 63

Query: 65  IAGRHAVLNALPFHRAVAVAGLCARLGVHYFDLTEDVASTHAIHALGRDARAVLMPQCGL 124
           ++G+ AVL+A PFH  VA+A   A   +HY DLTEDV ST  + A+  +AR   +PQCGL
Sbjct: 64  LSGKFAVLSAAPFHLTVAIAEAAAEAEIHYLDLTEDVESTRQVKAIAAEARTAFIPQCGL 123

Query: 125 APGFIGIVGNDLARRFDTLLDLRMRVGGLPRYPTNALRYNLYLEHRGADQRVLQSMRGAV 184
           APGFI IV NDL+R FDTL  +RMRVG LP+YP+NAL YNL     G     ++     V
Sbjct: 124 APGFISIVANDLSRHFDTLESVRMRVGALPQYPSNALNYNLTWSTDGVINEYIEPCEAIV 183

Query: 185 DGELVKVPPMEGYETFTLDGVEYEAFNTSGGLGTLPQTLLGKARNVDYKSVRYPGHCAIM 244
           +G L++VP ME  E F+LDGV YEAFNTSGGLGTL +TL GK R ++YK++RYPGH AI 
Sbjct: 184 EGSLIEVPAMEEREEFSLDGVTYEAFNTSGGLGTLCETLKGKVRTLNYKTIRYPGHAAIF 243

Query: 245 KLLLNDLRLRERRELLQDILESAIPATGQDVIVILATASGYRGGRLLQEAYSAHIHGDTV 304
           K LLNDL LR RRE+L+DILE+A+P T QDV+VI  T SG+R GRL+QE Y+  ++   V
Sbjct: 244 KALLNDLGLRHRREVLKDILENALPTTTQDVVVIFVTVSGFREGRLVQETYANKVYSGVV 303

Query: 305 DGHALSAIQLSTAAGICTALDLVVEGALPQRGFVGQESIPLDALLANRHGRIYA 358
            G   S IQ++TA  IC  LD++ EG +P +GFV QE I LD  LANR G  YA
Sbjct: 304 AGRMQSGIQITTAGSICAVLDMLAEGKIPTKGFVRQEDIALDTFLANRFGHYYA 357


Lambda     K      H
   0.323    0.139    0.405 

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: 352
Number of extensions: 12
Number of successful extensions: 2
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: 368
Length of database: 367
Length adjustment: 30
Effective length of query: 338
Effective length of database: 337
Effective search space:   113906
Effective search space used:   113906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 preprint 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