GapMind for Amino acid biosynthesis

 

Alignments for a candidate for moeZ in Phaeobacter inhibens BS107

Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate GFF2621 PGA1_c26620 putative molybdopterin biosynthesis protein MoeB

Query= SwissProt::P9WMN7
         (392 letters)



>FitnessBrowser__Phaeo:GFF2621
          Length = 378

 Score =  243 bits (619), Expect = 9e-69
 Identities = 127/246 (51%), Positives = 167/246 (67%), Gaps = 3/246 (1%)

Query: 16  SREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFD 75
           S  E+ RY+RH+++ +LG  GQK+L+ ARVLVIGAGGLGAP L YLAAAGVGTIG++D D
Sbjct: 102 SESELDRYARHIVLRELGGPGQKKLRKARVLVIGAGGLGAPALQYLAAAGVGTIGVIDDD 161

Query: 76  VVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYDL 135
           +V+ +NLQRQVIH   D+G  K  SA+ ++ A NP + VR +  RL    A DLF  YDL
Sbjct: 162 LVENANLQRQVIHRDQDIGIPKVFSAQAAMEAQNPYVTVRPYHRRLDADIATDLFGDYDL 221

Query: 136 ILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEPP 195
           ILDGTDNF TRYLVN  AV  GKP + G++ ++EGQ S+F    P   G  Y+ ++PE P
Sbjct: 222 ILDGTDNFETRYLVNRTAVALGKPLISGALSQWEGQISLF---HPTAGGPCYQCIFPEAP 278

Query: 196 PPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITIR 255
             G+ PSC+E GV+G +   V ++M  EAIK +TG G+TL G +L+YD L    R IT+ 
Sbjct: 279 AAGLAPSCSEAGVVGPLPGVVGAMMALEAIKAVTGAGQTLQGEILIYDGLYSESRKITLS 338

Query: 256 KDPSTP 261
           +    P
Sbjct: 339 QRSDCP 344


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: 461
Number of extensions: 35
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: 392
Length of database: 378
Length adjustment: 30
Effective length of query: 362
Effective length of database: 348
Effective search space:   125976
Effective search space used:   125976
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 (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