GapMind for Amino acid biosynthesis

 

Aligments for a candidate for moeZ in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate Echvi_1891 Echvi_1891 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2

Query= SwissProt::P9WMN7
         (392 letters)



>lcl|FitnessBrowser__Cola:Echvi_1891 Echvi_1891
           Dinucleotide-utilizing enzymes involved in molybdopterin
           and thiamine biosynthesis family 2
          Length = 360

 Score =  205 bits (521), Expect = 2e-57
 Identities = 128/363 (35%), Positives = 196/363 (53%), Gaps = 18/363 (4%)

Query: 22  RYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVVDESN 81
           RY + + +   G   Q +L ++ VL+IGAGGLG P   YL   GVGT+ I+D D V ESN
Sbjct: 5   RYQKQIRLKSFGKQSQDKLASSSVLIIGAGGLGTPVAQYLNGVGVGTLAIMDQDTVAESN 64

Query: 82  LQRQVIHGVADVGRSKAQSARDSIVAINPLIR-VRLHELRLAPSNAVDLFKQYDLILDGT 140
           L RQ +    DVG+ K       +   NP  R + + E  L P NA+     YDLI+D +
Sbjct: 65  LARQTLFTPEDVGKHKTDVLIQYLRRQNPSTRFINVREF-LTPVNALQELADYDLIVDAS 123

Query: 141 DNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVF-WEDAPDGLGVNYRDLYPEPPPPGM 199
           DNF TRYLVNDA V+  KP+++G+++ FEGQ SV  +++ P      YR L+PE   P  
Sbjct: 124 DNFGTRYLVNDACVMLDKPFIYGALHEFEGQVSVMNYQNGP-----TYRCLFPEVGDPSA 178

Query: 200 VPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITIRKDPS 259
           + +C E GVLGI+   + +    EA+K++TGIGE L G+LL+ D L  ++  + +   P 
Sbjct: 179 ILNCDENGVLGILPGLIGTYQALEAVKVLTGIGEPLAGKLLIIDTLAQTHLKVGLTSVPE 238

Query: 260 TPKITELVD-YEQFCGVVADDAAQAAKGSTITPRELRDWLDSGRKLALIDVRDPVEWDIV 318
              I +L + Y Q         +     +++T  E     +   +  +IDVR+  E+D  
Sbjct: 239 NQSIRKLQENYGQ------PMCSTDLPVTSLTCEEFWSKREGDSQHQIIDVRNEGEFDSG 292

Query: 319 HIDGAQLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEALAAVKKAGFSDAVH-LQGG 377
           H+D AQ IP S +   E   ++ +    +L C++G RS +A   ++       ++ L+GG
Sbjct: 293 HLDSAQNIPLSQLT--ERHQEINEKAPVILICQSGKRSLQAAQLLQSLHPEQIIYNLEGG 350

Query: 378 IVA 380
           + A
Sbjct: 351 MNA 353


Lambda     K      H
   0.319    0.137    0.404 

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: 356
Number of extensions: 22
Number of successful extensions: 4
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: 392
Length of database: 360
Length adjustment: 30
Effective length of query: 362
Effective length of database: 330
Effective search space:   119460
Effective search space used:   119460
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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